From 471dd08f14897d15df96e5db60208fcfaf7c9bd7 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 28 Feb 2018 18:23:57 +0000 Subject: Fixed issue that caused some GEMMA results to appear incorrectly --- wqflask/wqflask/marker_regression/gemma_mapping.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 68920130..54cde3c6 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -3,7 +3,7 @@ import os, math, string, random, json from base import webqtlConfig from base.trait import GeneralTrait from base.data_set import create_dataset -from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file +from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -11,7 +11,6 @@ logger = utility.logger.getLogger(__name__ ) def run_gemma(this_dataset, samples, vals, covariates, method, use_loco): """Generates p-values for each marker using GEMMA""" - assert_bin(GEMMA_COMMAND); if this_dataset.group.genofile != None: genofile_name = this_dataset.group.genofile[:-5] else: @@ -193,7 +192,7 @@ def parse_gemma_output(genofile_name): # if marker['chr'] != previous_chr: # previous_chr = marker['chr'] marker['Mb'] = float(line.split("\t")[2]) / 1000000 - marker['p_value'] = float(line.split("\t")[10]) + marker['p_value'] = float(line.split("\t")[11]) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 #marker['lrs_value'] = 0 @@ -203,7 +202,7 @@ def parse_gemma_output(genofile_name): marker_obs.append(marker) included_markers.append(line.split("\t")[1]) - p_values.append(float(line.split("\t")[10])) + p_values.append(float(line.split("\t")[11])) return marker_obs @@ -241,7 +240,7 @@ def parse_loco_output(this_dataset, gwa_output_filename): else: marker['chr'] = line.split("\t")[0] marker['Mb'] = float(line.split("\t")[2]) / 1000000 - marker['p_value'] = float(line.split("\t")[10]) + marker['p_value'] = float(line.split("\t")[11]) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 #marker['lrs_value'] = 0 @@ -251,6 +250,6 @@ def parse_loco_output(this_dataset, gwa_output_filename): marker_obs.append(marker) included_markers.append(line.split("\t")[1]) - p_values.append(float(line.split("\t")[10])) + p_values.append(float(line.split("\t")[11])) - return marker_obs + return marker_obs \ No newline at end of file -- cgit v1.2.3 From 67004cd8990ae97c0da234399721b5eb11b1675f Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 28 Feb 2018 18:28:12 +0000 Subject: Forgot to import function assert_file --- wqflask/wqflask/marker_regression/gemma_mapping.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 54cde3c6..2ed97303 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -3,7 +3,7 @@ import os, math, string, random, json from base import webqtlConfig from base.trait import GeneralTrait from base.data_set import create_dataset -from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR +from utility.tools import assert_file, flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR import utility.logger logger = utility.logger.getLogger(__name__ ) -- cgit v1.2.3 From e5992ce3e047fcfe79d66ed42c00c1af63438482 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 15 Mar 2018 17:59:35 +0000 Subject: Resolved conflicts --- .../wqflask/correlation_matrix/show_corr_matrix.py | 9 +- .../wqflask/marker_regression/marker_regression.py | 1 + .../marker_regression/marker_regression_gn1.py | 2 + .../wqflask/marker_regression/qtlreaper_mapping.py | 17 +- wqflask/wqflask/templates/correlation_matrix.html | 3 +- .../show_trait_calculate_correlations.html | 106 ++++++------ .../templates/show_trait_mapping_tools.html | 185 ++++++++++++++++++++- wqflask/wqflask/views.py | 2 +- 8 files changed, 250 insertions(+), 75 deletions(-) diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index b34beb7b..077386a3 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -173,9 +173,12 @@ class CorrelationMatrix(object): for sample in self.all_sample_list: groups.append(1) - pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) - - self.loadings_array = self.process_loadings() + try: + self.pca_works = "True" + pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) + self.loadings_array = self.process_loadings() + except: + self.pca_works = "False" self.js_data = dict(traits = [trait.name for trait in self.traits], groups = groups, diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 087b95b4..db4f8f46 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -228,6 +228,7 @@ class MarkerRegression(object): results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait, self.dataset, self.samples, + self.vals, self.json_data, self.num_perm, self.bootCheck, diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 211cf187..66884b0c 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -1204,6 +1204,8 @@ class MarkerRegression(object): else: if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": string2 = 'Using GEMMA mapping method with no control for other QTLs.' + if self.covariates != "": + string3 = 'Using following traits as covariates: ' + self.covariates elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": string2 = 'Using R/qtl mapping method with no control for other QTLs.' elif self.mapping_method == "plink": diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 50228b5e..6b58190f 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -1,17 +1,20 @@ -def gen_reaper_results(this_trait, dataset, samples_before, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): genotype = dataset.group.read_genotype_file() if manhattan_plot != True: genotype = genotype.addinterval() - samples, values, variances, sample_aliases = this_trait.export_informative() - trimmed_samples = [] trimmed_values = [] - for i in range(0, len(samples)): - if this_trait.data[samples[i]].name in samples_before: - trimmed_samples.append(samples[i]) - trimmed_values.append(values[i]) + for i in range(0, len(samples_before)): + try: + trimmed_values.append(float(trait_vals[i])) + trimmed_samples.append(samples_before[i]) + except: + pass perm_output = [] bootstrap_results = [] diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index ab793d58..d27788a8 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -61,6 +61,7 @@
+{% if pca_works == "True" %}

Factor Loadings Plot

@@ -93,7 +94,7 @@ - +{% endif %} {% endblock %} {% block js %} diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index c5f815ce..ef233333 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -1,9 +1,10 @@
+
- -
+ +
{% for tissue in corr_tools.dataset_menu %} {% if tissue.tissue %} @@ -37,8 +38,8 @@
- -
+ +
{% for group, pretty_group in sample_group_types.items() %} @@ -64,8 +65,8 @@
- -
+ +
- -
+ +
Chr:     Mb:  to  @@ -89,8 +90,8 @@
- -
+ +
@@ -103,48 +104,45 @@
- -
+ +
- -
- -
- - The Sample Correlation - is computed - between trait data and any - other traits in the sample database selected above. Use - Spearman - Rank - when the sample size is small (<20) or when there are influential outliers. - - - -
-
+
+
+ + The Sample Correlation + is computed + between trait data and any + other traits in the sample database selected above. Use + Spearman + Rank + when the sample size is small (<20) or when there are influential outliers. + + + +
\ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index dcec2b9e..60219cf5 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -1,6 +1,11 @@
+<<<<<<< HEAD {% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %}
+======= + {% if dataset.group.mapping_names|length > 0 %} +
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    @@ -41,8 +46,13 @@
    {% if genofiles and genofiles|length>0 %}
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    + +
    + + {% endif %} +
    +
    +
    + +
    +
    @@ -94,8 +139,13 @@
    {% if genofiles and genofiles|length>0 %}
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -162,8 +227,13 @@
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= +
    + +
    + +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    @@ -189,8 +268,13 @@
    {% if genofiles and genofiles|length>0 %}
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page +======= + +
    + +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -228,8 +323,13 @@
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +<<<<<<< HEAD
    +======= +
    + +
    + +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    @@ -295,8 +414,13 @@
    {% if genofiles and genofiles|length>0 %}
    +<<<<<<< HEAD
    +======= + +
    +>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page {% for item in genofiles %} @@ -62,24 +52,14 @@
    {% endif %}
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    +
    @@ -122,30 +95,29 @@
    +
    - +
    {% if genofiles and genofiles|length>0 %}
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -227,13 +184,8 @@
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    -<<<<<<< HEAD -
    -
    - -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    @@ -268,13 +212,8 @@
    {% if genofiles and genofiles|length>0 %}
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    -
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -323,13 +248,8 @@
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    -<<<<<<< HEAD -
    -
    - -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    @@ -414,13 +316,8 @@
    {% if genofiles and genofiles|length>0 %}
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page {% for item in genofiles %} @@ -502,33 +354,12 @@
    {% endif %}
    -<<<<<<< HEAD - -
    -=======
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
    -
    - -
    -<<<<<<< HEAD - - -
    -
    - -
    -
    -=======
    {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %} @@ -547,10 +378,10 @@
    ->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page +
    @@ -579,7 +410,7 @@
    -
    +
    {% if dataset.group.mapping_id == "1" %}
    GEMMA
    -- cgit v1.2.3 From 0bead53661ea701ffd9f9d565e4d2ecbbed81a8e Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 13 Apr 2018 15:55:56 +0000 Subject: Last commit didn't conflict for some reason, hopefully this one should --- wqflask/wqflask/marker_regression/gemma_mapping.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 4713f8d6..f28cc63e 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -3,11 +3,8 @@ import os, math, string, random, json from base import webqtlConfig from base.trait import GeneralTrait from base.data_set import create_dataset -<<<<<<< HEAD -from utility.tools import assert_file, flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR -======= + from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR ->>>>>>> 270f86c41f7c90cc4ca51bca0aec789a09a36a0e import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -251,4 +248,4 @@ def parse_loco_output(this_dataset, gwa_output_filename): included_markers.append(line.split("\t")[1]) p_values.append(float(line.split("\t")[11])) - return marker_obs \ No newline at end of file + return marker_obs -- cgit v1.2.3 From b3c2253a99ff9495a0132f466df825340ddf367c Mon Sep 17 00:00:00 2001 From: GN2 Date: Wed, 5 Sep 2018 03:38:46 -0500 Subject: Production updates --- .DS_Store | Bin 6148 -> 0 bytes .gitignore | 14 --- bin/genenetwork2 | 2 +- .../new/javascript/dataset_menu_structure.json | 95 ++++++++++++++++++--- 4 files changed, 85 insertions(+), 26 deletions(-) delete mode 100644 .DS_Store diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index d992942f..00000000 Binary files a/.DS_Store and /dev/null differ diff --git a/.gitignore b/.gitignore index 0006d9a8..0d20b648 100644 --- a/.gitignore +++ b/.gitignore @@ -1,15 +1 @@ -# gitignore *.pyc -*.orig -*.bak -*.cross -*~ -genotype_files/genotype/HSNIH_copy.geno -web/new_genotypes/HSNIH.json -wqflask/secure_server.py -build/ -dist/ -*.egg-info/ -EGG-INFO/ -wqflask/output/* -wqflask/wqflask/static/output/* diff --git a/bin/genenetwork2 b/bin/genenetwork2 index b3a8d8c2..006e87ba 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -210,7 +210,7 @@ if [ "$1" = '-gunicorn-prod' ] ; then echo PYTHONPATH=$PYTHONPATH if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi PID=$TMPDIR/gunicorn.$USER.pid - cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 1200 --max-requests 1000 --timeout 1200 wsgi" + cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 6000 --max-requests 1000 --timeout 1200 wsgi" echo RUNNING gunicorn $cmd gunicorn $cmd exit $? diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 81185136..d61168eb 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -2590,11 +2590,41 @@ ] ], "Liver mRNA": [ + [ + "852", + "NIA-AgBXD-Liv_HFD-0818", + "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **" + ], + [ + "857", + "EPFLMouseLiverCDHFDRMA0818", + "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" + ], + [ + "859", + "EPFLMouseLiverCDRMA0818", + "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" + ], + [ + "851", + "NIA-AgBXD-Liv_CDHFD-0818", + "NIA Aging BXD CD+HFD Liver Affy Clariom S Gene Level (Aug18) RMA **" + ], + [ + "853", + "NIA-AgBXD-Liv_CD-0818", + "NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA **" + ], [ "818", "UCLA_BXD_Liv_Jan16", "UCLA BXD Liver Affy M430 2.0 (Jan16) RMA" ], + [ + "858", + "EPFLMouseLiverHFDRMA0818", + "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" + ], [ "430", "EPFLMouseLiverRMA0413", @@ -2610,6 +2640,11 @@ "EPFLMouseLiverCDRMA0413", "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ], + [ + "848", + "EPFLMouseLiverHFCEx0413", + "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" + ], [ "433", "EPFLMouseLiverBothExRMA0413", @@ -2620,11 +2655,6 @@ "EPFLMouseLiverCDEx0413", "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" ], - [ - "848", - "EPFLMouseLiverHFCEx0413", - "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" - ], [ "700", "UTHSC-VGX_MmBXDHepatocytesRMA1014", @@ -3034,17 +3064,17 @@ [ "843", "UTHSC-BXD-Harv_Liv-0118", - "UTHSC BXD Harvested Liver RNA-Seq (Jan18) Log2 **" - ], - [ - "842", - "UTHSC-BXD-Liv-0917", - "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **" + "UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2 **" ], [ "850", "UTHSC-BXD-Liv-0818", "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA **" + ], + [ + "842", + "UTHSC-BXD-Liv-0917", + "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **" ] ], "Phenotypes": [ @@ -3658,12 +3688,43 @@ }, "rat": { "HSNIH-Palmer": { + "Hippocampus mRNA": [ + [ + "862", + "HSNIH-Rat-LHB-RSeq-0818", + "HSNIH-Palmer Lateral Habenula RNA-Seq (Aug18) rlog" + ] + ], + "Nucleus Accumbens mRNA": [ + [ + "860", + "HSNIH-Rat-Acbc-RSeq-0818", + "HSNIH-Palmer Nucleus Accumbens Core RNA-Seq (Aug18) rlog" + ] + ], "Phenotypes": [ [ "652", "HSNIH-PalmerPublish", "HSNIH-Palmer Published Phenotypes" ] + ], + "Prefrontal Cortex mRNA": [ + [ + "864", + "HSNIH-Rat-VoLo-RSeq-0818", + "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog" + ], + [ + "863", + "HSNIH-Rat-PL-RSeq-0818", + "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) rlog" + ], + [ + "861", + "HSNIH-Rat-IL-RSeq-0818", + "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) rlog" + ] ] }, "HSNIH-RGSMC": { @@ -5410,6 +5471,18 @@ [ "Phenotypes", "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Nucleus Accumbens mRNA", + "Nucleus Accumbens mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" ] ], "HSNIH-RGSMC": [ -- cgit v1.2.3 From 33e2e09d00881de9b07274bc52b58587e5135cab Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 5 Sep 2018 09:49:09 +0000 Subject: ELASTICSEARCH settings and fix runserver.py to run without gunicorn --- README.md | 12 +++++++++--- etc/default_settings.py | 10 +++++++++- wqflask/runserver.py | 4 ++++ wqflask/utility/tools.py | 1 + 4 files changed, 23 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 59645994..f0132e89 100644 --- a/README.md +++ b/README.md @@ -25,9 +25,15 @@ Once installed GN2 can be run online through a browser interface genenetwork2 ``` -(default is http://localhost:5003/). For full examples (you'll need to -set a number of environment variables), including running scripts and -a Python REPL, see the startup script +(default is http://localhost:5003/). A quick example is + +```sh +env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 GENENETWORK_FILES=~/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev +``` + +For full examples (you may need to set a number of environment +variables), including running scripts and a Python REPL, also see the +startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2). ## Testing diff --git a/etc/default_settings.py b/etc/default_settings.py index 3e54ad1f..85eab2c6 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -25,9 +25,17 @@ import os import sys GN_VERSION = open("../etc/VERSION","r").read() +GN_SERVER_URL = "http://localhost:8880/" # REST API server + +# ---- MySQL + SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" SQL_ALCHEMY_POOL_RECYCLE = 3600 -GN_SERVER_URL = "http://localhost:8880/" # REST API server + +# ---- Elastic search + +ELASTICSEARCH_HOST = "localhost" +ELASTICSEARCH_PORT = 9200 # ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 5f41d04d..c0ac980a 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -9,6 +9,7 @@ from wqflask import app + import logging import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -27,6 +28,9 @@ app_config() werkzeug_logger = logging.getLogger('werkzeug') +from utility.tools import WEBSERVER_MODE, SERVER_PORT +port = int(SERVER_PORT) + if WEBSERVER_MODE == 'DEBUG': app.run(host='0.0.0.0', port=port, diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index ea216a35..f12b0d76 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -233,6 +233,7 @@ def show_settings(): # Cached values GN_VERSION = get_setting('GN_VERSION') HOME = get_setting('HOME') +SERVER_PORT = get_setting('SERVER_PORT') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') GN_SERVER_URL = get_setting('GN_SERVER_URL') SQL_URI = get_setting('SQL_URI') -- cgit v1.2.3 From 92f505e42c6ac6314b29ac152654b393dc581501 Mon Sep 17 00:00:00 2001 From: Arthur Centeno Date: Sun, 26 Apr 2020 09:59:25 -0500 Subject: URL for finding services --- etc/default_settings.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/etc/default_settings.py b/etc/default_settings.py index 75f84dc4..4a35f42d 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -28,6 +28,8 @@ GN_VERSION = open("../etc/VERSION","r").read() SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" SQL_ALCHEMY_POOL_RECYCLE = 3600 GN_SERVER_URL = "http://localhost:8880/" # REST API server +GN2_BASE_URL = "http://genenetwork.org/" +GN2_BRANCH_URL = GN2_BASE_URL # ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True -- cgit v1.2.3 From f0139ef93c7e8329c1a84fe9f75273c36626df0e Mon Sep 17 00:00:00 2001 From: zsloan Date: Sun, 26 Apr 2020 10:57:09 -0500 Subject: Removed the code that was still writing the database menu JSON --- wqflask/base/data_set.py | 14 +++++--------- wqflask/wqflask/api/gen_menu.py | 5 ----- 2 files changed, 5 insertions(+), 14 deletions(-) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 8652e6b7..1f99df49 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -64,7 +64,7 @@ logger = getLogger(__name__ ) # Each subclass will add to this DS_NAME_MAP = {} -def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None): +def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None): if not dataset_type: dataset_type = Dataset_Getter(dataset_name) @@ -77,7 +77,7 @@ def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_sampleli class Dataset_Types(object): - def __init__(self, rebuild=False): + def __init__(self): """Create a dictionary of samples where the value is set to Geno, Publish or ProbeSet. E.g. @@ -93,13 +93,9 @@ Publish or ProbeSet. E.g. """ self.datasets = {} - if rebuild: #ZS: May make this the only option - data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) - #data = gen_menu.gen_dropdown_json() - else: - file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" - with open(file_name, 'r') as fh: - data = json.load(fh) + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) + #data = gen_menu.gen_dropdown_json() + for species in data['datasets']: for group in data['datasets'][species]: diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index 64a413c2..adf66fb5 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -36,11 +36,6 @@ def gen_dropdown_json(): types=types, datasets=datasets) - output_file = """./wqflask/static/new/javascript/dataset_menu_structure.json""" - - with open(output_file, 'w') as fh: - json.dump(data, fh, indent=3, sort_keys=True) - return data def get_species(): -- cgit v1.2.3 From e4a2db698b1103e7f6ed5c6e59946e343d3820f8 Mon Sep 17 00:00:00 2001 From: zsloan Date: Sun, 26 Apr 2020 10:59:24 -0500 Subject: Updated default_settings to include default GN2 base url --- etc/default_settings.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/etc/default_settings.py b/etc/default_settings.py index 75f84dc4..e01e4439 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -28,6 +28,7 @@ GN_VERSION = open("../etc/VERSION","r").read() SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" SQL_ALCHEMY_POOL_RECYCLE = 3600 GN_SERVER_URL = "http://localhost:8880/" # REST API server +GN2_BASE_URL = "http://genenetwork.org/" # Main GN2 URL # ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True @@ -43,13 +44,13 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a GITHUB_CLIENT_ID = "UNKNOWN" GITHUB_CLIENT_SECRET = "UNKNOWN" -GITHUB_AUTH_URL = "UNKNOWN" -GITHUB_API_URL = "UNKNOWN" +GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize" +GITHUB_API_URL = "https://api.github.com/user" ORCID_CLIENT_ID = "UNKNOWN" ORCID_CLIENT_SECRET = "UNKNOWN" -ORCID_AUTH_URL = "UNKNOWN" -ORCID_TOKEN_URL = "UNKNOWN" +ORCID_AUTH_URL = "https://orcid.org/oauth/authorize" +ORCID_TOKEN_URL = "https://orcid.org/oauth/token" ELASTICSEARCH_HOST = "localhost" ELASTICSEARCH_PORT = '9200' -- cgit v1.2.3 From cdcfb086de9277a1c1b2d8de57ceb78ae8683f53 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 26 Apr 2020 13:18:54 -0500 Subject: Updated menu --- .../new/javascript/dataset_menu_structure.json | 2655 ++++++++++++++++---- 1 file changed, 2220 insertions(+), 435 deletions(-) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index f9bce083..daf818b1 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -277,6 +277,18 @@ ] }, "CANDLE": { + "Methylation": [ + [ + "423", + "CANDLE_Meth27_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13)*" + ], + [ + "422", + "CANDLE_Meth_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13) Z-Score*" + ] + ], "Newborn Cord Blood mRNA": [ [ "324", @@ -307,7 +319,7 @@ ] }, "GTEx": { - "Adipose tissue, subcutaneous mRNA": [ + "Adipose Tissue, Subcutaneous mRNA": [ [ "580", "GTEx_log2_Subcu_0314", @@ -319,7 +331,7 @@ "GTEx Human Subcutaneous (Apr14) RPKM" ] ], - "Adipose tissue, visceral mRNA": [ + "Adipose Tissue, Visceral mRNA": [ [ "587", "GTEx_log2_Visce_0314", @@ -873,14 +885,14 @@ ] }, "GTEx_v5": { - "Adipose tissue, subcutaneous mRNA": [ + "Adipose Tissue, Subcutaneous mRNA": [ [ "718", "GTEXv5_AdipSub_0915", "GTEXv5 Human Adipose Subcutaneous RefSeq (Sep15) RPKM log2" ] ], - "Adipose tissue, visceral mRNA": [ + "Adipose Tissue, Visceral mRNA": [ [ "719", "GTEXv5_AdiVis_0915", @@ -1252,253 +1264,857 @@ ] ] }, - "HB": { - "Cerebellum mRNA": [ + "GTEx_v8": { + "Adipose Tissue, Subcutaneous mRNA": [ [ - "326", - "HBTRC-MLC_0611", - "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" + "950", + "GTEXv8_AdipSub_tpm_0220", + "GTEXv8 Human Adipose Subcutaneous RNA-Seq (Feb20) TPM log2" ], [ - "361", - "HBTRC-MLC_N_0611", - "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" + "901", + "GTEXv8_AdipSub_0220", + "GTEXv8 Human Adipose Subcutaneous RNA-Seq (Feb20) log2" + ] + ], + "Adipose Tissue, Visceral mRNA": [ + [ + "951", + "GTEXv8_AdiVis_tpm_0220", + "GTEXv8 Human Adipose Visceral Omentum RNA-Seq (Feb20) TPM log2" ], [ - "362", - "HBTRC-MLC_AD_0611", - "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" + "902", + "GTEXv8_AdiVis_0220", + "GTEXv8 Human Adipose Visceral Omentum RNA-Seq (Feb20) log2" + ] + ], + "Adrenal Gland mRNA": [ + [ + "952", + "GTEXv8_AdrGla_tpm_0220", + "GTEXv8 Human Adrenal Gland RNA-Seq (Feb20) TPM log2" ], [ - "363", - "HBTRC-MLC_HD_0611", - "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" + "903", + "GTEXv8_AdrGla_0220", + "GTEXv8 Human Adrenal Gland RNA-Seq (Feb20) log2" ] ], - "Prefrontal Cortex mRNA": [ + "Amygdala mRNA": [ [ - "328", - "HBTRC-MLPFC_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" + "956", + "GTEXv8_Amy_tpm_0220", + "GTEXv8 Human Brain Amygdala RNA-Seq (Feb20) TPM log2" ], [ - "367", - "HBTRC-MLPFC_N_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" + "907", + "GTEXv8_Amy_0220", + "GTEXv8 Human Brain Amygdala RNA-Seq (Feb20) log2" + ] + ], + "Anterior Cingulate Cortex mRNA": [ + [ + "957", + "GTEXv8_AntCtx_tpm_0220", + "GTEXv8 Human Brain Anterior cingulate cortex BA24 RNA-Seq (Feb20) TPM log2" ], [ - "368", - "HBTRC-MLPFC_AD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" + "908", + "GTEXv8_AntCtx_0220", + "GTEXv8 Human Brain Anterior cingulate cortex BA24 RNA-Seq (Feb20) log2" + ] + ], + "Aorta mRNA": [ + [ + "953", + "GTEXv8_ArtAor_tpm_0220", + "GTEXv8 Human Artery Aorta RNA-Seq (Feb20) TPM log2" ], [ - "369", - "HBTRC-MLPFC_HD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" + "904", + "GTEXv8_ArtAor_0220", + "GTEXv8 Human Artery Aorta RNA-Seq (Feb20) log2" ] ], - "Primary Visual Cortex mRNA": [ + "Breast - Mammary Tissue mRNA": [ [ - "327", - "HBTRC-MLVC_0611", - "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" + "969", + "GTEXv8_BrMa_tpm_0220", + "GTEXv8 Human Breast Mammary Tissue RNA-Seq (Feb20) TPM log2" ], [ - "364", - "HBTRC-MLVC_N_0611", - "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" + "920", + "GTEXv8_BrMa_0220", + "GTEXv8 Human Breast Mammary Tissue RNA-Seq (Feb20) log2" + ] + ], + "Caudate mRNA": [ + [ + "958", + "GTEXv8_BrCa_tpm_0220", + "GTEXv8 Human Brain Caudate basal ganglia RNA-Seq (Feb20) TPM log2" ], [ - "365", - "HBTRC-MLVC_AD_0611", - "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" + "909", + "GTEXv8_BrCa_0220", + "GTEXv8 Human Brain Caudate basal ganglia RNA-Seq (Feb20) log2" + ] + ], + "Cells - EBV-Transformed Lymphocytes mRNA": [ + [ + "970", + "GTEXv8_EBV_tpm_0220", + "GTEXv8 Human Cells-EBV-transformed lymphocytes RNA-Seq (Feb20) TPM log2" ], [ - "366", - "HBTRC-MLVC_HD_0611", - "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" + "921", + "GTEXv8_EBV_0220", + "GTEXv8 Human Cells-EBV-transformed lymphocytes RNA-Seq (Feb20) log2" ] - ] - }, - "HCP": { - "Phenotypes": [ + ], + "Cells - Transformed Fibroblasts mRNA": [ [ - "None", - "HCPPublish", - "HCP Private Phenotypes" + "971", + "GTEXv8_CTF_tpm_0220", + "GTEXv8 Human Cells-Transformed fibroblasts RNA-Seq (Feb20) TPM log2" + ], + [ + "922", + "GTEXv8_CTF_0220", + "GTEXv8 Human Cells-Transformed fibroblasts RNA-Seq (Feb20) log2" ] - ] - }, - "HLC": { - "Liver mRNA": [ + ], + "Cerebellar Cortex mRNA": [ [ - "320", - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" + "961", + "GTEXv8_BrCtx_tpm_0220", + "GTEXv8 Human Brain Cortex RNA-Seq (Feb20) TPM log2" ], [ - "384", - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" + "912", + "GTEXv8_BrCtx_0220", + "GTEXv8 Human Brain Cortex RNA-Seq (Feb20) log2" + ] + ], + "Cerebellar Hemisphere mRNA": [ + [ + "959", + "GTEXv8_CerH_tpm_0220", + "GTEXv8 Human Brain Cerebellar Hemisphere RNA-Seq (Feb20) TPM log2" ], [ - "383", - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" + "910", + "GTEXv8_CerH_0220", + "GTEXv8 Human Brain Cerebellar Hemisphere RNA-Seq (Feb20) log2" ] ], - "Phenotypes": [ + "Cerebellum mRNA": [ [ - "635", - "HLCPublish", - "HLC Published Phenotypes" + "960", + "GTEXv8_BrCe_tpm_0220", + "GTEXv8 Human Brain Cerebellum RNA-Seq (Feb20) TPM log2" + ], + [ + "911", + "GTEXv8_BrCe_0220", + "GTEXv8 Human Brain Cerebellum RNA-Seq (Feb20) log2" ] - ] - }, - "HLT": { - "Lung mRNA": [ + ], + "Colon - Sigmoid mRNA": [ [ - "455", - "GSE23546HLT0613", - "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + "972", + "GTEXv8_ColSig_tpm_0220", + "GTEXv8 Human Colon-Sigmoid RNA-Seq (Feb20) TPM log2" ], [ - "454", - "GRNG-GSE23545HLT0613", - "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + "923", + "GTEXv8_ColSig_0220", + "GTEXv8 Human Colon-Sigmoid RNA-Seq (Feb20) log2" ] - ] - }, - "HSB": { - "Amygdala mRNA": [ + ], + "Colon - Transverse mRNA": [ [ - "330", - "KIN_YSM_AMY_0711", - "GN330 Human Amygdala Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "973", + "GTEXv8_ColTra_tpm_0220", + "GTEXv8 Human Colon-Transverse RNA-Seq (Feb20) TPM log2" + ], + [ + "924", + "GTEXv8_ColTra_0220", + "GTEXv8 Human Colon-Transverse RNA-Seq (Feb20) log2" ] ], - "Cerebellar Cortex mRNA": [ + "Coronary mRNA": [ [ - "331", - "KIN_YSM_CBC_0711", - "Human Cerebellar Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "954", + "GTEXv8_ArtCor_tpm_0220", + "GTEXv8 Human Artery Coronary RNA-Seq (Feb20) TPM log2" + ], + [ + "905", + "GTEXv8_ArtCor_0220", + "GTEXv8 Human Artery Coronary RNA-Seq (Feb20) log2" ] ], - "Dorsolateral Prefrontal Cortex mRNA": [ + "Esophagus - Gastroesophageal mRNA": [ [ - "333", - "KIN_YSM_DFC_0711", - "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "974", + "GTEXv8_GastJun_tpm_0220", + "GTEXv8 Human Esophagus - Gastroesophageal Junction RNA-Seq (Feb20) TPM log2" + ], + [ + "925", + "GTEXv8_GastJun_0220", + "GTEXv8 Human Esophagus - Gastroesophageal Junction RNA-Seq (Feb20) log2" ] ], - "Hippocampus mRNA": [ + "Esophagus - Mucosa mRNA": [ [ - "337", - "KIN_YSM_HIP_0711", - "Human Hippocampus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "975", + "GTEXv8_EsoMu_tpm_0220", + "GTEXv8 Human Esophagus-Mucosa RNA-Seq (Feb20) TPM log2" + ], + [ + "926", + "GTEXv8_EsoMu_0220", + "GTEXv8 Human Esophagus-Mucosa RNA-Seq (Feb20) log2" ] ], - "Inferior Temporal Cortex mRNA": [ + "Esophagus - Muscularis mRNA": [ [ - "339", - "KIN_YSM_ITC_0711", - "Human Inferior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "976", + "GTEXv8_EsoMus_tpm_0220", + "GTEXv8 Human Esophagus-Muscularis RNA-Seq (Feb20) TPM log2" + ], + [ + "927", + "GTEXv8_EsoMus_0220", + "GTEXv8 Human Esophagus-Muscularis RNA-Seq (Feb20) log2" ] ], - "Medial Prefrontal Cortex mRNA": [ + "Frontal Cortex mRNA": [ [ - "343", - "KIN_YSM_MFC_0711", - "Human Medial Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "962", + "GTEXv8_BrFr_tpm_0220", + "GTEXv8 Human Brain Frontal Cortex BA9 RNA-Seq (Feb20) TPM log2" + ], + [ + "913", + "GTEXv8_BrFr_0220", + "GTEXv8 Human Brain Frontal Cortex BA9 RNA-Seq (Feb20) log2" ] ], - "Mediodorsal Nucleus of Thalamus mRNA": [ + "Heart - Atrial Appendage mRNA": [ [ - "342", - "KIN_YSM_MD_0711", - "Human Mediodorsal Nucleus of Thalamus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "977", + "GTEXv8_HAA_tpm_0220", + "GTEXv8 Human Heart-Atrial Appendage RNA-Seq (Feb20) TPM log2" + ], + [ + "928", + "GTEXv8_HAA_0220", + "GTEXv8 Human Heart-Atrial Appendage RNA-Seq (Feb20) log2" ] ], - "Orbital Prefrontal Cortex mRNA": [ + "Heart - Left Ventricle mRNA": [ [ - "347", - "KIN_YSM_OFC_0711", - "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "978", + "GTEXv8_LV_tpm_0220", + "GTEXv8 Human Heart-Left Ventricle RNA-Seq (Feb20) TPM log2" + ], + [ + "929", + "GTEXv8_LV_0220", + "GTEXv8 Human Heart-Left Ventricle RNA-Seq (Feb20) log2" ] ], - "Phenotypes": [ + "Hippocampus mRNA": [ [ - "None", - "HSBPublish", - "HSB Published Phenotypes" + "963", + "GTEXv8_Hip_tpm_0220", + "GTEXv8 Human Brain Hippocampus RNA-Seq (Feb20) TPM log2" + ], + [ + "914", + "GTEXv8_Hip_0220", + "GTEXv8 Human Brain Hippocampus RNA-Seq (Feb20) log2" ] ], - "Posterior Inferior Parietal Cortex mRNA": [ + "Hypothalamus mRNA": [ [ - "338", - "KIN_YSM_IPC_0711", - "Human Posterior Inferior Parietal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "964", + "GTEXv8_Hiptha_tpm_0220", + "GTEXv8 Human Brain Hypothalamus RNA-Seq (Feb20) TPM log2" + ], + [ + "915", + "GTEXv8_Hiptha_0220", + "GTEXv8 Human Brain Hypothalamus RNA-Seq (Feb20) log2" ] ], - "Posterior Superior Temporal Cortex mRNA": [ + "Kidney mRNA": [ [ - "350", - "KIN_YSM_STC_0711", - "Human Posterior Superior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "979", + "GTEXv8_Kidn_tpm_0220", + "GTEXv8 Human Kidney-Cortex RNA-Seq (Feb20) TPM log2" + ], + [ + "930", + "GTEXv8_Kidn_0220", + "GTEXv8 Human Kidney-Cortex RNA-Seq (Feb20) log2" ] ], - "Primary Auditory (A1) Cortex mRNA": [ + "Liver mRNA": [ [ - "329", - "KIN_YSM_A1C_0711", - "Human Primary Auditory (A1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "980", + "GTEXv8_Liv_tpm_0220", + "GTEXv8 Human Liver RNA-Seq (Feb20) TPM log2" + ], + [ + "931", + "GTEXv8_Liv_0220", + "GTEXv8 Human Liver RNA-Seq (Feb20) log2" ] ], - "Primary Motor (M1) Cortex mRNA": [ + "Lung mRNA": [ [ - "341", - "KIN_YSM_M1C_0711", - "Human Primary Motor (M1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "981", + "GTEXv8_Lung_tpm_0220", + "GTEXv8 Human Lung RNA-Seq (Feb20) TPM log2" + ], + [ + "932", + "GTEXv8_Lung_0220", + "GTEXv8 Human Lung RNA-Seq (Feb20) log2" ] ], - "Primary Somatosensory (S1) Cortex mRNA": [ + "Muscle mRNA": [ [ - "349", - "KIN_YSM_S1C_0711", - "Human Primary Somatosensory (S1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "982", + "GTEXv8_MuSk_tpm_0220", + "GTEXv8 Human Muscle-Skeletal RNA-Seq (Feb20) TPM log2" + ], + [ + "933", + "GTEXv8_MuSk_0220", + "GTEXv8 Human Muscle-Skeletal RNA-Seq (Feb20) log2" ] ], - "Primary Visual Cortex mRNA": [ + "Nerve - Tibial mRNA": [ [ - "354", - "KIN_YSM_V1C_0711", - "Human Primary Visual Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "983", + "GTEXv8_Tib_tpm_0220", + "GTEXv8 Human Nerve-Tibial RNA-Seq (Feb20) TPM log2" + ], + [ + "934", + "GTEXv8_Tib_0220", + "GTEXv8 Human Nerve-Tibial RNA-Seq (Feb20) log2" ] ], - "Striatum mRNA": [ + "Nucleus Accumbens mRNA": [ [ - "351", - "KIN_YSM_STR_0711", - "Human Striatum Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "965", + "GTEXv8_NuAcc_tpm_0220", + "GTEXv8 Human Brain Nucleus accumbens basal ganglia RNA-Seq (Feb20) TPM log2" + ], + [ + "916", + "GTEXv8_NuAcc_0220", + "GTEXv8 Human Brain Nucleus accumbens basal ganglia RNA-Seq (Feb20) log2" ] ], - "Ventrolateral Prefrontal Cortex mRNA": [ + "Ovary mRNA": [ [ - "356", - "KIN_YSM_VFC_0711", - "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + "984", + "GTEXv8_Ov_tpm_0220", + "GTEXv8 Human Ovary RNA-Seq (Feb20) TPM log2" + ], + [ + "935", + "GTEXv8_Ov_0220", + "GTEXv8 Human Ovary RNA-Seq (Feb20) log2" ] - ] - }, - "Islets-Gerling": { + ], + "Pancreas mRNA": [ + [ + "985", + "GTEXv8_Panc_tpm_0220", + "GTEXv8 Human Pancreas RNA-Seq (Feb20) TPM log2" + ], + [ + "936", + "GTEXv8_Panc_0220", + "GTEXv8 Human Pancreas RNA-Seq (Feb20) log2" + ] + ], "Phenotypes": [ [ "None", - "Islets-GerlingPublish", - "Islets-Gerling Phenotypes" + "GTEx_v8Publish", + "GTEx_v8 Phenotypes" ] - ] - }, + ], + "Pituitary Gland mRNA": [ + [ + "986", + "GTEXv8_Pit_tpm_0220", + "GTEXv8 Human Pituitary RNA-Seq (Feb20) TPM log2" + ], + [ + "937", + "GTEXv8_Pit_0220", + "GTEXv8 Human Pituitary RNA-Seq (Feb20) log2" + ] + ], + "Prostate mRNA": [ + [ + "987", + "GTEXv8_Prost_tpm_0220", + "GTEXv8 Human Prostate RNA-Seq (Feb20) TPM log2" + ], + [ + "938", + "GTEXv8_Prost_0220", + "GTEXv8 Human Prostate RNA-Seq (Feb20) log2" + ] + ], + "Putamen mRNA": [ + [ + "966", + "GTEXv8_PutB_tpm_0220", + "GTEXv8 Human Brain Putamen basal ganglia RNA-Seq (Feb20) TPM log2" + ], + [ + "917", + "GTEXv8_PutB_0220", + "GTEXv8 Human Brain Putamen basal ganglia RNA-Seq (Feb20) log2" + ] + ], + "Salivary Gland mRNA": [ + [ + "988", + "GTEXv8_SalGl_tpm_0220", + "GTEXv8 Human Salivary Gland Minor RNA-Seq (Feb20) TPM log2" + ], + [ + "939", + "GTEXv8_SalGl_0220", + "GTEXv8 Human Salivary Gland Minor RNA-Seq (Feb20) log2" + ] + ], + "Skin - Not Sun Exposed (Suprapubic) mRNA": [ + [ + "989", + "GTEXv8_SkN_tpm_0220", + "GTEXv8 Human Skin-Not Sun Exposed-Suprapubic RNA-Seq (Feb20) TPM log2" + ], + [ + "940", + "GTEXv8_SkN_0220", + "GTEXv8 Human Skin-Not Sun Exposed-Suprapubic RNA-Seq (Feb20) log2" + ] + ], + "Skin - Sun Exposed (Lower leg) mRNA": [ + [ + "990", + "GTEXv8_SkS_tpm_0220", + "GTEXv8 Human Skin-Sun Exposed-Lower leg RNA-Seq (Feb20) TPM log2" + ], + [ + "941", + "GTEXv8_SkS_0220", + "GTEXv8 Human Skin-Sun Exposed-Lower leg RNA-Seq (Feb20) log2" + ] + ], + "Small Intestine - Terminal Ileum mRNA": [ + [ + "997", + "GTEXv8_SInt_tpm_0220", + "GTEXv8 Human Small Intestine - Terminal Ileum RNA-Seq (Feb20) TPM log2" + ], + [ + "948", + "GTEXv8_SInt_0220", + "GTEXv8 Human Small Intestine - Terminal Ileum RNA-Seq (Feb20) log2" + ] + ], + "Spinal Cord mRNA": [ + [ + "967", + "GTEXv8_SpCo_tpm_0220", + "GTEXv8 Human Brain Spinal cord cervical c-1 RNA-Seq (Feb20) TPM log2" + ], + [ + "918", + "GTEXv8_SpCo_0220", + "GTEXv8 Human Brain Spinal cord cervical c-1 RNA-Seq (Feb20) log2" + ] + ], + "Spleen mRNA": [ + [ + "991", + "GTEXv8_Sple_tpm_0220", + "GTEXv8 Human Spleen RNA-Seq (Feb20) TPM log2" + ], + [ + "942", + "GTEXv8_Sple_0220", + "GTEXv8 Human Spleen RNA-Seq (Feb20) log2" + ] + ], + "Stomach mRNA": [ + [ + "992", + "GTEXv8_Sto_tpm_0220", + "GTEXv8 Human Stomach RNA-Seq (Feb20) TPM log2" + ], + [ + "943", + "GTEXv8_Sto_0220", + "GTEXv8 Human Stomach RNA-Seq (Feb20) log2" + ] + ], + "Substantia Nigra mRNA": [ + [ + "968", + "GTEXv8_SubN_tpm_0220", + "GTEXv8 Human Brain Substantia nigra RNA-Seq (Feb20) TPM log2" + ], + [ + "919", + "GTEXv8_SubN_0220", + "GTEXv8 Human Brain Substantia nigra RNA-Seq (Feb20) log2" + ] + ], + "Testis mRNA": [ + [ + "993", + "GTEXv8_Test_tpm_0220", + "GTEXv8 Human Testis RNA-Seq (Feb20) TPM log2" + ], + [ + "944", + "GTEXv8_Test_0220", + "GTEXv8 Human Testis RNA-Seq (Feb20) log2" + ] + ], + "Thyroid mRNA": [ + [ + "994", + "GTEXv8_Thy_tpm_0220", + "GTEXv8 Human Thyroid RNA-Seq (Feb20) TPM log2" + ], + [ + "945", + "GTEXv8_Thy_0220", + "GTEXv8 Human Thyroid RNA-Seq (Feb20) log2" + ] + ], + "Tibial mRNA": [ + [ + "955", + "GTEXv8_ArtTib_tpm_0220", + "GTEXv8 Human Artery Tibial RNA-Seq (Feb20) TPM log2" + ], + [ + "906", + "GTEXv8_ArtTib_0220", + "GTEXv8 Human Artery Tibial RNA-Seq (Feb20) log2" + ] + ], + "Uterus mRNA": [ + [ + "995", + "GTEXv8_Ut_tpm_0220", + "GTEXv8 Human Uterus RNA-Seq (Feb20) TPM log2" + ], + [ + "946", + "GTEXv8_Ut_0220", + "GTEXv8 Human Uterus RNA-Seq (Feb20) log2" + ] + ], + "Vagina mRNA": [ + [ + "996", + "GTEXv8_Vag_tpm_0220", + "GTEXv8 Human Vagina RNA-Seq (Feb20) TPM log2" + ], + [ + "947", + "GTEXv8_Vag_0220", + "GTEXv8 Human Vagina RNA-Seq (Feb20) log2" + ] + ], + "Whole Blood mRNA": [ + [ + "998", + "GTEXv8_Wbl_tpm_0220", + "GTEXv8 Human Whole Blood RNA-Seq (Feb20) TPM log2" + ], + [ + "949", + "GTEXv8_Wbl_0220", + "GTEXv8 Human Whole Blood RNA-Seq (Feb20) log2" + ] + ] + }, + "HB": { + "Cerebellum mRNA": [ + [ + "326", + "HBTRC-MLC_0611", + "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" + ], + [ + "361", + "HBTRC-MLC_N_0611", + "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" + ], + [ + "362", + "HBTRC-MLC_AD_0611", + "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" + ], + [ + "363", + "HBTRC-MLC_HD_0611", + "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "328", + "HBTRC-MLPFC_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" + ], + [ + "367", + "HBTRC-MLPFC_N_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" + ], + [ + "368", + "HBTRC-MLPFC_AD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" + ], + [ + "369", + "HBTRC-MLPFC_HD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" + ] + ], + "Primary Visual Cortex mRNA": [ + [ + "327", + "HBTRC-MLVC_0611", + "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" + ], + [ + "364", + "HBTRC-MLVC_N_0611", + "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" + ], + [ + "365", + "HBTRC-MLVC_AD_0611", + "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" + ], + [ + "366", + "HBTRC-MLVC_HD_0611", + "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" + ] + ] + }, + "HCP": { + "Phenotypes": [ + [ + "None", + "HCPPublish", + "HCP Private Phenotypes" + ] + ] + }, + "HLC": { + "Liver mRNA": [ + [ + "320", + "HLC_0311", + "GSE9588 Human Liver Normal (Mar11) Both Sexes" + ], + [ + "384", + "HLCF_0311", + "GSE9588 Human Liver Normal (Mar11) Females" + ], + [ + "383", + "HLCM_0311", + "GSE9588 Human Liver Normal (Mar11) Males" + ] + ], + "Phenotypes": [ + [ + "635", + "HLCPublish", + "HLC Published Phenotypes" + ] + ] + }, + "HLT": { + "Lung mRNA": [ + [ + "455", + "GSE23546HLT0613", + "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ], + [ + "454", + "GRNG-GSE23545HLT0613", + "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ] + ] + }, + "HSB": { + "Amygdala mRNA": [ + [ + "330", + "KIN_YSM_AMY_0711", + "GN330 Human Amygdala Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Cerebellar Cortex mRNA": [ + [ + "331", + "KIN_YSM_CBC_0711", + "Human Cerebellar Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Dorsolateral Prefrontal Cortex mRNA": [ + [ + "333", + "KIN_YSM_DFC_0711", + "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Hippocampus mRNA": [ + [ + "337", + "KIN_YSM_HIP_0711", + "Human Hippocampus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Inferior Temporal Cortex mRNA": [ + [ + "339", + "KIN_YSM_ITC_0711", + "Human Inferior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Medial Prefrontal Cortex mRNA": [ + [ + "343", + "KIN_YSM_MFC_0711", + "Human Medial Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Mediodorsal Nucleus of Thalamus mRNA": [ + [ + "342", + "KIN_YSM_MD_0711", + "Human Mediodorsal Nucleus of Thalamus Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Orbital Prefrontal Cortex mRNA": [ + [ + "347", + "KIN_YSM_OFC_0711", + "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Phenotypes": [ + [ + "None", + "HSBPublish", + "HSB Published Phenotypes" + ] + ], + "Posterior Inferior Parietal Cortex mRNA": [ + [ + "338", + "KIN_YSM_IPC_0711", + "Human Posterior Inferior Parietal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Posterior Superior Temporal Cortex mRNA": [ + [ + "350", + "KIN_YSM_STC_0711", + "Human Posterior Superior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Auditory (A1) Cortex mRNA": [ + [ + "329", + "KIN_YSM_A1C_0711", + "Human Primary Auditory (A1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Motor (M1) Cortex mRNA": [ + [ + "341", + "KIN_YSM_M1C_0711", + "Human Primary Motor (M1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Somatosensory (S1) Cortex mRNA": [ + [ + "349", + "KIN_YSM_S1C_0711", + "Human Primary Somatosensory (S1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Primary Visual Cortex mRNA": [ + [ + "354", + "KIN_YSM_V1C_0711", + "Human Primary Visual Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Striatum mRNA": [ + [ + "351", + "KIN_YSM_STR_0711", + "Human Striatum Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ], + "Ventrolateral Prefrontal Cortex mRNA": [ + [ + "356", + "KIN_YSM_VFC_0711", + "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" + ] + ] + }, + "Islets-Gerling": { + "Islets mRNA": [ + [ + "824", + "UTHSC_HuIslets_Mar17", + "UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA" + ] + ], + "Phenotypes": [ + [ + "None", + "Islets-GerlingPublish", + "Islets-Gerling Phenotypes" + ] + ] + }, "TIGEM-Retina-RNA-Seq": { "Phenotypes": [ [ @@ -1516,95 +2132,46 @@ ] } }, - "mouse": { - "AIL": { - "Genotypes": [ + "macaque monkey": { + "Macaca-fasicularis": { + "Amygdala mRNA": [ [ - "None", - "AILGeno", - "AIL Genotypes" + "255", + "INIA_MacFas_AMG_RMA_0110", + "INIA Macaca fasicularis Amygdala (Jan10) RMA" ] ], - "Hippocampus mRNA": [ - [ - "874", - "UCSD_AIL_HIP_RNA-Seq_log2_0418", - "UCSD AIL Hippocampus (Apr18) RNA-Seq Log2" - ], + "Brain mRNA": [ [ - "844", - "UCSD_AIL_HIP_RNA-Seq_0418", - "UCSD AIL Hippocampus (Apr18) RNA-Seq" + "251", + "INIA_MacFas_brain_RMA_0110", + "INIA Macaca fasicularis Brain (Jan10) RMA" ] ], - "Phenotypes": [ + "Hippocampus mRNA": [ [ - "653", - "AILPublish", - "AIL Phenotypes" + "254", + "INIA_MacFas_Hc_RMA_0110", + "INIA Macaca fasicularis Hippocampus (Jan10) RMA" ] ], - "Prefrontal Cortex mRNA": [ - [ - "876", - "UCSD_AIL_PFC_RNA-Seq_log2_0418", - "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq Log2" - ], + "Nucleus Accumbens mRNA": [ [ - "846", - "UCSD_AIL_PFC_RNA-Seq_0418", - "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq" + "253", + "INIA_MacFas_Ac_RMA_0110", + "INIA Macaca fasicularis Nucleus Accumbens (Jan10) RMA" ] ], - "Striatum mRNA": [ - [ - "875", - "UCSD_AIL_STR_RNA-Seq_log2_0418", - "UCSD AIL Striatum (Apr18) RNA-Seq Log2" - ], - [ - "845", - "UCSD_AIL_STR_RNA-Seq_0418", - "UCSD AIL Striatum (Apr18) RNA-Seq" - ] - ] - }, - "AIL-LGSM-F34-A": { - "Phenotypes": [ - [ - "655", - "AIL-LGSM-F34-APublish", - "AIL F34-A Phenotypes" - ] - ] - }, - "AIL-LGSM-F34-F39-43-GBS": { - "Phenotypes": [ - [ - "654", - "AIL-LGSM-F34-F39-43-GBSPublish", - "AIL F34-F39-43-GBS Phenotypes" - ] - ] - }, - "AIL-LGSM-F34-GBS": { - "Phenotypes": [ - [ - "656", - "AIL-LGSM-F34-GBSPublish", - "AIL F34-GBS Phenotypes" - ] - ] - }, - "AIL-LGSM-F39-43-GBS": { - "Phenotypes": [ + "Prefrontal Cortex mRNA": [ [ - "657", - "AIL-LGSM-F39-43-GBSPublish", - "AIL F39-43-GBS Phenotypes" + "252", + "INIA_MacFas_Pf_RMA_0110", + "INIA Macaca fasicularis Prefrontal Cortex (Jan10) RMA" ] ] - }, + } + }, + "mouse": { "AKXD": { "Genotypes": [ [ @@ -1685,6 +2252,22 @@ ] ] }, + "B6-Lens": { + "Ocular Lens mRNA": [ + [ + "999", + "MouseB6Lens_rma_0220", + "Mouse Ocular Lens Developmental Timecourse (Feb20) RMA" + ] + ], + "Phenotypes": [ + [ + "None", + "B6-LensPublish", + "B6-Lens Phenotypes" + ] + ] + }, "B6BTBRF2": { "Genotypes": [ [ @@ -1720,6 +2303,25 @@ "B6D2Publish", "UTHSC-Glaucoma-Aged-Retina Phenotypes" ] + ], + "Retina mRNA": [ + [ + "803", + "UTHSC_mm9_B6D2_Ret_0916", + "UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA" + ], + [ + "804", + "UTHSC_mm9_B6D2_RetEx_0916", + "UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Exon Level RMA" + ] + ], + "Retina microRNA": [ + [ + "806", + "UTHSC_mm10_B6D2_Ret_miRNA_1116", + "UTHSC B6D2 Retina Affy miRNA-4.0 (Nov16) RMA" + ] ] }, "B6D2F2": { @@ -1771,6 +2373,28 @@ "B6D2F2-PSU Genotypes" ] ], + "Muscle mRNA": [ + [ + "134", + "PSU-B6D2F2_0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA" + ], + [ + "404", + "PSU-B6D2F2_F0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Females" + ], + [ + "405", + "PSU-B6D2F2_M0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males" + ], + [ + "406", + "PSU-B6D2F2_M2000812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males Aged 200*" + ] + ], "Phenotypes": [ [ "None", @@ -1906,6 +2530,23 @@ "UCLA BHF2 Liver (June05) mlratio" ] ], + "Muscle mRNA": [ + [ + "203", + "UCLA_BHF2_MUSCLE_FEMALE", + "UCLA BHF2 Muscle Female mlratio*" + ], + [ + "202", + "UCLA_BHF2_MUSCLE_MALE", + "UCLA BHF2 Muscle Male mlratio*" + ], + [ + "168", + "UCLA_BHF2_MUSCLE_0605", + "UCLA BHF2 Muscle (June05) mlratio*" + ] + ], "Phenotypes": [ [ "None", @@ -2090,6 +2731,26 @@ "414", "UCLA_BXD-on_Femur_0113_RSN", "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v1.1 (Jan13) RSN" + ], + [ + "464", + "UTHSCWGU88BFMG1013", + "UTHSC WGU88 Male Bone Femur AFFY Mouse Gene ST 2.0 Gene Level (Oct13) RMA" + ], + [ + "465", + "UTHSCWGU88BFMEx1013", + "UTHSC WGU88 Male Bone Femur AFFY Mouse Gene ST 2.0 Exon Level (Oct13) RMA" + ], + [ + "466", + "UTHSCWGU88BFFG1013", + "UTHSC WGU88 Female Bone Femur AFFY Mouse Gene ST 2.0 Gene Level (Oct13) RMA" + ], + [ + "467", + "UTHSCWGU88BFFEx1013", + "UTHSC WGU88 Female Bone Femur AFFY Mouse Gene ST 2.0 Exon Level (Oct13) RMA" ] ], "Brain mRNA": [ @@ -2221,6 +2882,76 @@ "9", "CB_M_1003_M", "SJUT Cerebellum mRNA M430 (Oct03) MAS5" + ], + [ + "436", + "CMMTUBCBXDCerILM0513", + "UBC/CMMT BXD Cerebellum All Ages Combined ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "441", + "CMMTUBCBXDG12CerILM0513", + "UBC/CMMT BXD E12 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "442", + "CMMTUBCBXDG15CerILM0513", + "UBC/CMMT BXD E15 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "443", + "CMMTUBCBXDG18CerILM0513", + "UBC/CMMT BXD E18 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "437", + "CMMTUBCBXDP00CerILM0513", + "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "438", + "CMMTUBCBXDP03CerILM0513", + "UBC/CMMT BXD P3 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "439", + "CMMTUBCBXDP06CerILM0513", + "UBC/CMMT BXD P6 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "440", + "CMMTUBCBXDP09CerILM0513", + "UBC/CMMT BXD P9 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" + ], + [ + "415", + "GenEx_BXD_CerebEt_RMA_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes" + ], + [ + "416", + "GenEx_BXD_CerebEt_RMA_F_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Females" + ], + [ + "417", + "GenEx_BXD_CerebEt_RMA_M_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Males" + ], + [ + "418", + "GenEx_BXD_CerebSal_RMA_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes" + ], + [ + "419", + "GenEx_BXD_CerebSal_RMA_F_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Females" + ], + [ + "420", + "GenEx_BXD_CerebSal_RMA_M_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Males" ] ], "Eye mRNA": [ @@ -2297,6 +3028,21 @@ "597", "UTHSC_GutExL_0414", "UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Exon Level (Apr14) RMA" + ], + [ + "839", + "EPFL-LISP_BXD_Col-CD+HFD0917", + "EPFL/LISP BXD CD+HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA" + ], + [ + "841", + "EPFL-LISP_BXD_Col-HFD0917", + "EPFL/LISP BXD HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA" + ], + [ + "840", + "EPFL-LISP_BXD_Col-CD0917", + "EPFL/LISP BXD CD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA" ] ], "Genotypes": [ @@ -2502,6 +3248,23 @@ "711", "UTHSC_BXD_AgeHipp0515", "UTHSC BXD Aged Hippocampus Affy MoGene1.0 ST (May15) RMA Gene Level" + ], + [ + "393", + "UTHSC_BXD_HArev3_0912", + "UTHSC BXD Aged Hippocampus rev3 Affy Mouse Gene 1.0 ST (Sep12) RMA" + ], + [ + "392", + "UTHSC_BXD_H_0912", + "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA Exon Level" + ] + ], + "Hippocampus microRNA": [ + [ + "491", + "UTHSC_BXD_Hip_miRNASeq0214", + "UTHSC BXD Hippocampus Ion Torrent microRNA (Feb14) RPKM*" ] ], "Hypothalamus mRNA": [ @@ -2578,6 +3341,30 @@ "Mouse Kidney M430v2 (Jul06) PDNN" ] ], + "Leucocytes mRNA": [ + [ + "218", + "Illum_BXD_PBL_1108", + "UWA Illumina PBL (Nov08) RSN*" + ] + ], + "Liver DNAm": [ + [ + "891", + "UTHSC-BXD-LivDNAm-1119", + "UTHSC BXD Liver CD-HFD DNAm (Nov19) Sesame" + ], + [ + "892", + "UTHSC-BXD-LivHFDNAm-1119", + "UTHSC BXD Liver HFD DNAm (Nov19) Sesame" + ], + [ + "893", + "UTHSC-BXD-LivCDNAm-1119", + "UTHSC BXD Liver CD DNAm (Nov19) Sesame" + ] + ], "Liver Metabolome": [ [ "835", @@ -2616,6 +3403,21 @@ ] ], "Liver Proteome": [ + [ + "887", + "EPFL-ETHZ-BXD-LivProtAvg-CD-HF-1119", + "EPFL/ETHZ BXD Liver Proteome CD+HFD (Nov19)" + ], + [ + "888", + "EPFL-ETHZ-BXD-LivProtAvg-CD-1119", + "EPFL/ETHZ BXD Liver Proteome CD (Nov19)" + ], + [ + "889", + "EPFL-ETHZ-BXD-LivProtAvg-HFD-1119", + "EPFL/ETHZ BXD Liver Proteome HFD (Nov19)" + ], [ "540", "EPFLETHZBXDprotCD0514", @@ -2683,6 +3485,21 @@ "NIA-AgBXD-Liv_CD-rna-seq-0818", "NIA Aging BXD CD Liver RNA-Seq (Aug18) Log2" ], + [ + "851", + "NIA-AgBXD-Liv_CDHFD-0818", + "NIA Aging BXD CD+HFD Liver Affy Clariom S Gene Level (Aug18) RMA" + ], + [ + "852", + "NIA-AgBXD-Liv_HFD-0818", + "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA" + ], + [ + "853", + "NIA-AgBXD-Liv_CD-0818", + "NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA" + ], [ "818", "UCLA_BXD_Liv_Jan16", @@ -2799,6 +3616,26 @@ "161", "HZI_0408_M", "HZI Lung M430v2 (Apr08) MAS5" + ], + [ + "807", + "HZI_LungBXD_RNA-Seq_1116", + "HZI Lung Flu Infected BXD (Nov16) RNA-Seq*" + ], + [ + "598", + "HZI_PR8M-F_1014", + "HZI PR8M-Infected Lungs Females RNAseq (Oct14) RPKM Log2*" + ], + [ + "387", + "HZI_PR8M_Q_0612", + "HZI PR8M-Infected Lungs Agilent4x44 (Apr12) Quantile Females" + ], + [ + "424", + "HZI_LTCF_0313", + "HZI Lung Time Course Flu PR8M (Mar13) Schughart*" ] ], "Midbrain mRNA": [ @@ -2808,6 +3645,23 @@ "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile" ] ], + "Muscle Metabolome": [ + [ + "476", + "EPFL-LISP_MusPMetCDHFD1213", + "EPFL/LISP BXD Muscle Polar Metabolites CD+HFD (Jun14)" + ], + [ + "477", + "EPFL-LISP_MusPMetHFD1213", + "EPFL/LISP BXD Muscle Polar Metabolites HFD (Jun14)" + ], + [ + "478", + "EPFL-LISP_MusPMetCD1213", + "EPFL/LISP BXD Muscle Polar Metabolites CD (Jun14)" + ] + ], "Muscle mRNA": [ [ "378", @@ -2877,11 +3731,68 @@ "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" ] ], + "Neutrophils mRNA": [ + [ + "595", + "UTHSC-Neut-1014", + "UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) RMA" + ], + [ + "596", + "UTHSC-Neut_EL-1014", + "UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) RMA Exon Level" + ] + ], "Nucleus Accumbens mRNA": [ [ "156", "VCUSalo_1007_R", "VCU BXD NAc Sal M430 2.0 (Oct07) RMA" + ], + [ + "792", + "VCU_BXD_Nac_CIE_Air_0416", + "VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "793", + "VCU_BXD_Nac_CIE_AirZ_0416", + "VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "794", + "VCU_BXD_Nac_CIE_Et_0416", + "VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "795", + "VCU_BXD_Nac_CIE_EtZ_0416", + "VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "155", + "VCUEtOH_1007_R", + "VCU BXD NAc EtOH M430 2.0 (Oct07) RMA" + ], + [ + "154", + "VCUSal_1007_R", + "VCU BXD NAc EtOH vs Sal M430 2.0 (Oct07) Sscore*" + ], + [ + "409", + "VCU_NAc_Air_0113_R", + "VCU BXD NAc CIE Air M430 2.0 (Jan13) RMA" + ], + [ + "408", + "VCU_NAc_Et_0113_R", + "VCU BXD NAc CIE EtOH M430 2.0 (Jan13) RMA" + ], + [ + "407", + "VCU_NAc_AvE_0113_Ss", + "VCU BXD NAc EtOH vs CIE Air M430 2.0 (Jan13) Sscore*" ] ], "Phenotypes": [ @@ -2918,7 +3829,44 @@ "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Exon Level" ] ], + "Popliteal Lymph Node mRNA": [ + [ + "390", + "STJ_PLN_0912", + "St Jude BXD Popliteal Lymph Node Affy HT MG-430 PM (Sep12) RMA" + ] + ], "Prefrontal Cortex mRNA": [ + [ + "898", + "DOD-BXD-PFC-CD-RNA-Seq-ComB-1019", + "DOD BXD PFC GWI CD RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "899", + "DOD-BXD-PFC-CTL-RNA-Seq-ComB-1019", + "DOD BXD PFC GWI CTL RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "900", + "DOD-BXD-PFC-DFP-RNA-Seq-ComB-1019", + "DOD BXD PFC GWI DFP RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "883", + "DOD-BXD-PFC-CD-RNA-Seq-1019", + "DOD BXD PFC GWI CD RNA-Seq (Oct19) TPM Log2" + ], + [ + "884", + "DOD-BXD-PFC-CTL-RNA-Seq-1019", + "DOD BXD PFC GWI CTL RNA-Seq (Oct19) TPM Log2" + ], + [ + "885", + "DOD-BXD-PFC-DFP-RNA-Seq-1019", + "DOD BXD PFC GWI DFP RNA-Seq (Oct19) TPM Log2" + ], [ "135", "VCUSal_1206_R", @@ -2933,6 +3881,41 @@ "137", "VCUSal_1006_R", "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" + ], + [ + "788", + "VCU_BXD_PFC_CIE_Air_0416", + "VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "789", + "VCU_BXD_PFC_CIE_AirZ_0416", + "VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "790", + "VCU_BXD_PFC_CIE_Et_0416", + "VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA" + ], + [ + "791", + "VCU_BXD_PFC_CIE_EtZ_0416", + "VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score" + ], + [ + "299", + "VCU_PF_AvE_0111_Ss", + "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore*" + ], + [ + "300", + "VCU_PF_Et_0111_R", + "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA" + ], + [ + "301", + "VCU_PF_Air_0111_R", + "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA" ] ], "Retina mRNA": [ @@ -2971,11 +3954,26 @@ "DoDTATRCRetBLMoGene2E_0316", "DoD Retina After Blast Affy MoGene 2.0 ST (Mar16) RMA Exon Level" ], + [ + "796", + "DoDRetBlastvsNormalEx_0416", + "DoD Retina Blast vs Normal Retina Affy MoGene 2.0 ST (Apr16) RMA Exon Level" + ], [ "385", "ONCRetILM6_0412", "ONC HEI Retina (April 2012) RankInv" ], + [ + "386", + "B6D2ONCILM_0412", + "B6D2 ONC Retina (April 2012) RankInv" + ], + [ + "372", + "G2HEIONCRetILM6_0911", + "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv" + ], [ "371", "HEIONCvsCRetILM6_0911", @@ -3027,6 +4025,11 @@ "227", "IoP_SPL_RMA_0509", "IoP Affy MOE 430v2 Spleen (May09) RMA" + ], + [ + "216", + "Illum_BXD_Spl_1108", + "UWA Illumina Spleen (Nov08) RSN*" ] ], "Striatum mRNA": [ @@ -3105,6 +4108,13 @@ "HZI Treg M430v2 (Feb11) RMA" ] ], + "Thymus mRNA": [ + [ + "217", + "Illum_BXD_Thy_1108", + "UWA Illumina Thymus (Nov08) RSN*" + ] + ], "Ventral Tegmental Area mRNA": [ [ "228", @@ -3140,28 +4150,52 @@ "BXD-Harvested Genotypes" ] ], - "Hippocampus mRNA": [ + "Hippocampus Proteome": [ [ "873", "JAX-BXD-Hip-Pro-0219", "JAX BXD Hippocampal Proteome (Feb19)" ] ], + "Liver DNAm": [ + [ + "890", + "INIA-BXD-LivDNAm-1119", + "INIA BXD Liver DNAm CD-HFD (Nov19) Sesame" + ] + ], + "Liver Proteome": [ + [ + "886", + "EPFL-ETHZ-BXD-LivProtCD-HF-1119", + "EPFL/ETHZ BXD Liver Proteome CD-HFD (Nov19)" + ] + ], "Liver mRNA": [ [ "877", "UTHSC-BXD-Harv_Liv-1019", "UTHSC BXD Harvested Liver RNA-Seq (Oct19) TPM Log2" ], + [ + "850", + "UTHSC-BXD-Liv-0818", + "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA" + ], [ "843", "UTHSC-BXD-Harv_Liv-0118", "UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2" + ], + [ + "842", + "UTHSC-BXD-Liv-0917", + "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA" ] ], "Phenotypes": [ [ - "None", + "660", "BXD-HarvestedPublish", "BXD-NIA-Longevity Phenotypes" ] @@ -3263,6 +4297,29 @@ ] ] }, + "CC": { + "Genotypes": [ + [ + "663", + "CCGeno", + "CC Genotypes" + ] + ], + "Midbrain mRNA": [ + [ + "894", + "LSRU-CC-ST-1219", + "LSRU CC Male Midbrain RNA-Seq (Dec19) TPM Log2" + ] + ], + "Phenotypes": [ + [ + "662", + "CCPublish", + "CC Phenotypes" + ] + ] + }, "CFW": { "Hippocampus mRNA": [ [ @@ -3360,9 +4417,35 @@ "CIE-RMAPublish", "CIE-RMA Phenotypes" ] + ], + "Prefrontal Cortex mRNA": [ + [ + "832", + "INIA_UTHSC_PFC_AffyMTA1_May17", + "INIA-UTHSC Prefrontal Cortex CIE Affy MTA 1.0 GeneLevel (Apr17) RMA" + ] + ], + "Striatum mRNA": [ + [ + "833", + "INIA_UTHSC_Str_AffyMTA1_May17", + "INIA-UTHSC Striatum CIE Affy MTA 1.0 GeneLevel (Apr17) RMA" + ] ] }, "CMS": { + "Hippocampus mRNA": [ + [ + "771", + "CMS_Hipp1115", + "Hippocampus Mouse Transcriptome Assay 1.0 Gene Level Main (Nov15) RMA" + ], + [ + "800", + "CMS_Hipp_ZScr_1115", + "Hippocampus Mouse Transcriptome Assay 1.0 Gene Level Z-Score (Nov15) RMA" + ] + ], "Phenotypes": [ [ "None", @@ -3520,6 +4603,92 @@ ] ] }, + "DOD-BXD-GWI": { + "Genotypes": [ + [ + "None", + "DOD-BXD-GWIGeno", + "DOD-BXD-GWI Genotypes" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "895", + "DOD-BXD-Ind-PFC-CD-RNA-Seq-ComB-1019", + "DOD BXD INDV PFC GWI CD RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "896", + "DOD-BXD-Ind-PFC-CTL-RNA-Seq-ComB-1019", + "DOD BXD INDV PFC GWI CTL RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "897", + "DOD-BXD-Ind-PFC-DFP-RNA-Seq-ComB-1019", + "DOD BXD INDV PFC GWI DFP RNA-Seq ComB (Dec19) TPM Log2" + ], + [ + "880", + "DOD-BXD-Ind-PFC-CD-RNA-Seq-1019", + "DOD BXD INDV PFC GWI CD RNA-Seq (Oct19) TPM Log2" + ], + [ + "881", + "DOD-BXD-Ind-PFC-CTL-RNA-Seq-1019", + "DOD BXD INDV PFC GWI CTL RNA-Seq (Oct19) TPM Log2" + ], + [ + "882", + "DOD-BXD-Ind-PFC-DFP-RNA-Seq-1019", + "DOD BXD INDV PFC GWI DFP RNA-Seq (Oct19) TPM Log2" + ] + ] + }, + "EMSR": { + "Hippocampus mRNA": [ + [ + "825", + "UTHSC_EMSR_All_AffyMTA1_Mar17", + "UTHSC Hippocampus All Treatments Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "826", + "UTHSC_EMSR_Sal_AffyMTA1_Mar17", + "UTHSC Hippocampus Saline Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "827", + "UTHSC_EMSR_Et_AffyMTA1_Mar17", + "UTHSC Hippocampus Ethanol Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "828", + "UTHSC_EMSR_St_AffyMTA1_Mar17", + "UTHSC Hippocampus Stress Affy MTA 1.0 Gene Level (Mar17) RMA" + ], + [ + "829", + "UTHSC_EMSR_EtSt_AffyMTA1_Mar17", + "UTHSC Hippocampus Ethanol-Stress Affy MTA 1.0 Gene Level (Mar17) RMA" + ] + ] + }, + "HET3-ITP": { + "Genotypes": [ + [ + "None", + "HET3-ITPGeno", + "HET3-ITP Genotypes" + ] + ], + "Phenotypes": [ + [ + "661", + "HET3-ITPPublish", + "HET3 ITP Longevity Phenotypes" + ] + ] + }, "HS": { "Hippocampus mRNA": [ [ @@ -3559,16 +4728,123 @@ ] ] }, - "LGSM-AIG34_50-56-GBS": { + "JAX-D2-Mono-RNA-Seq": { + "Retina mRNA": [ + [ + "878", + "JAX-D2-Mono1vPBMC-Ret-RNA-Seq-0619", + "JAX DBA/2J Monocyte 1 vs PBMC RNA-Seq (Jun19)" + ], + [ + "879", + "JAX-D2-Mono2vPBMC-Ret-RNA-Seq-0619", + "JAX DBA/2J Monocyte 2 vs PBMC RNA-Seq (Jun19)" + ] + ] + }, + "LGSM-AI": { + "Hippocampus mRNA": [ + [ + "874", + "UCSD_AIL_HIP_RNA-Seq_log2_0418", + "UCSD AIL Hippocampus (Apr18) RNA-Seq Log2" + ], + [ + "844", + "UCSD_AIL_HIP_RNA-Seq_0418", + "UCSD AIL Hippocampus (Apr18) RNA-Seq" + ] + ], "Phenotypes": [ [ "None", + "LGSM-AIPublish", + "LGSM AI Phenotypes" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "876", + "UCSD_AIL_PFC_RNA-Seq_log2_0418", + "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq Log2" + ], + [ + "846", + "UCSD_AIL_PFC_RNA-Seq_0418", + "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq" + ] + ], + "Striatum mRNA": [ + [ + "875", + "UCSD_AIL_STR_RNA-Seq_log2_0418", + "UCSD AIL Striatum (Apr18) RNA-Seq Log2" + ], + [ + "845", + "UCSD_AIL_STR_RNA-Seq_0418", + "UCSD AIL Striatum (Apr18) RNA-Seq" + ] + ] + }, + "LGSM-AI-G34-A": { + "Phenotypes": [ + [ + "655", + "LGSM-AI-G34-APublish", + "LGSM AI G34 Phenotypes" + ] + ] + }, + "LGSM-AI-G34-GBS": { + "Phenotypes": [ + [ + "656", + "LGSM-AI-G34-GBSPublish", + "LGSM AI G34 GBS Phenotypes" + ] + ] + }, + "LGSM-AI-G34_39-43-GBS": { + "Phenotypes": [ + [ + "657", + "LGSM-AI-G34_39-43-GBSPublish", + "LGSM AI G34 G39-43 GBS Phenotypes" + ] + ] + }, + "LGSM-AI-G39-43-GBS": { + "Phenotypes": [ + [ + "654", + "LGSM-AI-G39-43-GBSPublish", + "LGSM AI G39-43 GBS Phenotypes" + ] + ] + }, + "LGSM-AIG34_50-56-GBS": { + "Phenotypes": [ + [ + "659", "LGSM-AIG34_50-56-GBSPublish", - "LGSM AIG34/50-56 GBS Phenotypes" + "LGSM AI G34/50-56 GBS Phenotypes" ] ] }, "LXS": { + "Brain mRNA": [ + [ + "783", + "UCAMC_LXSBrEtOH_RNA-Seq_0216", + "UCAMC LXS Whole Brain Ethanol RNA Sequence (Feb16) FPKM*" + ], + [ + "784", + "UCAMC_LXSBrSal_RNA-Seq_0216", + "UCAMC LXS Whole Brain Saline RNA Sequence (Feb16) FPKM*" + ] + ], "Genotypes": [ [ "601", @@ -3650,6 +4926,16 @@ "130", "VCUSal_0806_R", "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" + ], + [ + "132", + "VCUEt_vs_Sal_0806_R", + "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore*" + ], + [ + "131", + "VCUEtOH_0806_R", + "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA" ] ] }, @@ -3701,6 +4987,11 @@ "273", "UMUTAffyExon_0209_RMA_MDP", "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" + ], + [ + "594", + "UFL-MDP-Hipp0814", + "UFL MDP Hippocampus Antidepressant Affy Mouse 430 2.0 (Aug14) RMA" ] ], "Liver mRNA": [ @@ -3795,6 +5086,36 @@ "SOTNOT-OHSU Genotypes" ] ] + }, + "Scripps-2013": { + "Anterior Cingulate Cortex mRNA": [ + [ + "450", + "ScrBXDACC4G0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Gene Level" + ], + [ + "451", + "ScrBXDACC4GEx0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Exon Level" + ] + ] + }, + "UTHSC-Cannabinoid": { + "Genotypes": [ + [ + "None", + "UTHSC-CannabinoidGeno", + "UTHSC-Cannabinoid Genotypes" + ] + ], + "Phenotypes": [ + [ + "None", + "UTHSC-CannabinoidPublish", + "UTHSC Cannabinoid Pilot Phenotypes" + ] + ] } }, "poplar": { @@ -3809,22 +5130,6 @@ } }, "rat": { - "HRDP": { - "Genotypes": [ - [ - "None", - "HRDPGeno", - "HRDP Genotypes" - ] - ], - "Phenotypes": [ - [ - "None", - "HRDPPublish", - "HRDP Phenotypes" - ] - ] - }, "HSNIH-Palmer": { "Infralimbic Cortex mRNA": [ [ @@ -4011,295 +5316,411 @@ "arabidopsis": [ [ "BayXSha", - "BayXSha" + "BayXSha", + "Family:None" ], [ "ColXBur", - "ColXBur" + "ColXBur", + "Family:None" ], [ "ColXCvi", - "ColXCvi" + "ColXCvi", + "Family:None" ] ], "barley": [ [ "QSM", - "QSM" + "QSM", + "Family:None" ], [ "SXM", - "SXM" + "SXM", + "Family:None" ] ], "drosophila": [ [ "DGRP", - "Drosophila Genetic Reference Panel" + "Drosophila Genetic Reference Panel", + "Family:None" ], [ "Oregon-R_x_2b3", - "Oregon-R x 2b3" + "Oregon-R x 2b3", + "Family:None" ] ], "human": [ [ "HB", - "Brain, Aging: AD, HD, Normal Gene Expression (Harvard/Merck)" + "Brain, Aging: AD, HD, Normal Gene Expression (Harvard/Merck)", + "Family:None" ], [ "AD-cases-controls", - "Brain, Aging: AD, Normal Gene Expression (Liang)" + "Brain, Aging: AD, Normal Gene Expression (Liang)", + "Family:None" ], [ "AD-cases-controls-Myers", - "Brain, Aging: AD, Normal Gene Expression with Genotypes (Myers)" + "Brain, Aging: AD, Normal Gene Expression with Genotypes (Myers)", + "Family:None" ], [ "Aging-Brain-UCI", - "Brain, Aging: Normal Gene Expression (UCI/Cotman)" + "Brain, Aging: Normal Gene Expression (UCI/Cotman)", + "Family:None" ], [ "HCP", - "Brain, Cognition, Human Connectome Project" + "Brain, Cognition, Human Connectome Project", + "Family:None" ], [ "HSB", - "Brain, Development: Normal Gene Expression (Yale/Sestan)" + "Brain, Development: Normal Gene Expression (Yale/Sestan)", + "Family:None" ], [ "Brain-Normal-NIH-Gibbs", - "Brain: Normal Gene Expression (NIH/Gibbs)" + "Brain: Normal Gene Expression (NIH/Gibbs)", + "Family:None" ], [ "CANDLE", - "Child Development: CANDLE Cohort with Genotypes (TUCI/UTHSC)" + "Child Development: CANDLE Cohort with Genotypes (TUCI/UTHSC)", + "Family:None" ], [ "GTEx", - "GTEx v3 All Tissues, RNA-Seq with Genotypes" + "GTEx v3 All Tissues, RNA-Seq with Genotypes", + "Family:None" ], [ "GTEx_v5", - "GTEx v5 All Tissues, RNA-Seq with Genotypes" + "GTEx v5 All Tissues, RNA-Seq with Genotypes", + "Family:None" + ], + [ + "GTEx_v8", + "GTEx v8 All Tissues, RNA-Seq without Genotypes", + "Family:None" ], [ "HLC", - "Liver: Normal Gene Expression with Genotypes (Merck)" + "Liver: Normal Gene Expression with Genotypes (Merck)", + "Family:None" ], [ "HLT", - "Lung: Normal Gene Expression (Merck)" + "Lung: Normal Gene Expression (Merck)", + "Family:None" ], [ "CEPH-2004", - "Lymphoblastoid Cells: Gene Expression (CEPH, Williams)" + "Lymphoblastoid Cells: Gene Expression (CEPH, Williams)", + "Family:None" ], [ "Islets-Gerling", - "Pancreatic: Islets (UTHSC/Gerling)" + "Pancreatic: Islets (UTHSC/Gerling)", + "Family:None" ], [ "TIGEM-Retina-RNA-Seq", - "Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)" + "Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)", + "Family:None" + ] + ], + "macaque monkey": [ + [ + "Macaca-fasicularis", + "Macaca fasicularis (Cynomolgus monkey)", + "Family:None" ] ], "mouse": [ [ - "AIL", - "AIL Advanced Intercross Line" + "AKXD", + "AKXD Family", + "Family:Reference Populations" + ], + [ + "AXBXA", + "AXB/BXA Family", + "Family:Reference Populations" + ], + [ + "BXD", + "BXD Family", + "Family:Reference Populations" + ], + [ + "BXH", + "BXH Family", + "Family:Reference Populations" + ], + [ + "CC", + "CC Family", + "Family:Reference Populations" + ], + [ + "CXB", + "CXB Family", + "Family:Reference Populations" + ], + [ + "LXS", + "ILSXISS (LXS) Family", + "Family:Reference Populations" + ], + [ + "MDP", + "Mouse Diversity Panel", + "Family:Reference Populations" + ], + [ + "B6D2RI", + "BXD Aged Hippocampus", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F34-A", - "AIL LGSM F34 (Array)" + "BXD-Bone", + "BXD Bone Individual Data", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F34-GBS", - "AIL LGSM F34 (GBS)" + "DOD-BXD-GWI", + "BXD DOD Gulf War Illness", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F34-F39-43-GBS", - "AIL LGSM F34 and F39-43 (GBS)" + "BXD-Harvested", + "BXD NIA Longevity Study", + "Family:BXD Individual Data" ], [ - "AIL-LGSM-F39-43-GBS", - "AIL LGSM F39-43 (GBS)" + "UTHSC-Cannabinoid", + "BXD UTHSC Cannabinoid Pilot", + "Family:BXD Individual Data" ], [ - "AKXD", - "AKXD RI Family" + "B6BTBRF2", + "B6BTBRF2", + "Family:Crosses, AIL, HS" ], [ - "AXBXA", - "AXB/BXA RI Family" + "BHHBF2", + "B6C3HF2 UCLA Metabolism", + "Family:Crosses, AIL, HS" ], [ - "B6BTBRF2", - "B6BTBRF2" + "BHF2", + "B6C3HF2(APOE-) UCLA Metabolism", + "Family:Crosses, AIL, HS" ], [ "Linsenbardt-Boehm", - "B6D2 EtOH Selected Advanced Intercross" + "B6D2 EtOH Selected Advanced Intercross", + "Family:Crosses, AIL, HS" ], [ "B6D2F2", - "B6D2F2" - ], - [ - "B6D2F2-PSU", - "B6D2F2 PSU" + "B6D2F2 OHSU Brain", + "Family:Crosses, AIL, HS" ], [ - "BDF2-1999", - "BDF2 UCLA" + "BDF2-2005", + "B6D2F2 OHSU Striatum", + "Family:Crosses, AIL, HS" ], [ - "BDF2-2005", - "BDF2-2005" + "B6D2F2-PSU", + "B6D2F2 PSU Muscle", + "Family:Crosses, AIL, HS" ], [ - "BHHBF2", - "BH/HB F2 UCLA" + "BDF2-1999", + "B6D2F2 UCLA Liver", + "Family:Crosses, AIL, HS" ], [ - "BHF2", - "BHF2 (Apoe Null) UCLA" + "CTB6F2", + "CastB6/B6Cast F2 UCLA", + "Family:Crosses, AIL, HS" ], [ - "B6D2RI", - "BXD Aged" + "CFW", + "CFW Outbred GWAS", + "Family:Crosses, AIL, HS" ], [ - "BXD-Bone", - "BXD Bone Individual Data" + "HET3-ITP", + "HET3 ITP Longevity", + "Family:Crosses, AIL, HS" ], [ - "BXD-Harvested", - "BXD NIA Longevity Study" + "HS", + "Heterogeneous Stock", + "Family:Crosses, AIL, HS" ], [ - "BXD", - "BXD RI Family" + "HS-CC", + "Heterogeneous Stock Collaborative Cross", + "Family:Crosses, AIL, HS" ], [ - "BXD300", - "BXD300" + "LGSM-AI-G34_39-43-GBS", + "LGSM AI G34 G39-43 Palmer (GBS)", + "Family:Crosses, AIL, HS" ], [ - "BXH", - "BXH RI Family" + "LGSM-AI-G34-A", + "LGSM AI G34 Palmer (Array)", + "Family:Crosses, AIL, HS" ], [ - "CTB6F2", - "CastB6/B6Cast F2 UCLA" + "LGSM-AI-G34-GBS", + "LGSM AI G34 Palmer (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CFW", - "CFW Outbred GWAS" + "LGSM-AIG34_50-56-GBS", + "LGSM AI G34/50-56 Lionikas (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CIE-INIA", - "Chronic Intermittent Ethanol Phase 1" + "LGSM-AI-G39-43-GBS", + "LGSM AI G39-43 Palmer (GBS)", + "Family:Crosses, AIL, HS" ], [ - "CIE-RMA", - "Chronic Intermittent Ethanol Phase 2" + "LGSM-AI", + "LGSM AI Palmer", + "Family:Crosses, AIL, HS" ], [ - "CMS", - "Chronic Mild Stress" + "SOTNOT-OHSU", + "SOTNOT-OHSU", + "Family:Crosses, AIL, HS" ], [ - "CXB", - "CXB RI Family (strain means)" + "B6-Lens", + "B6 Lens", + "Family:Non-genetic Cohort" ], [ - "D2GM", - "D2 Glaucoma Model" + "CIE-INIA", + "Chronic Intermittent Ethanol Phase 1", + "Family:Non-genetic Cohort" ], [ - "B6D2", - "Glaucoma and Aged Retina, UTHSC" + "CIE-RMA", + "Chronic Intermittent Ethanol Phase 2", + "Family:Non-genetic Cohort" ], [ - "HS", - "Heterogeneous Stock" + "CMS", + "Chronic Mild Stress", + "Family:Non-genetic Cohort" ], [ - "HS-CC", - "Heterogeneous Stock Collaborative Cross" + "D2GM", + "D2 Glaucoma Model", + "Family:Non-genetic Cohort" ], [ - "LXS", - "ILSXISS (LXS) RI Family (strain means)" + "JAX-D2-Mono-RNA-Seq", + "D2 Glaucoma Monocyte JAX", + "Family:Non-genetic Cohort" ], [ - "LGSM-AIG34_50-56-GBS", - "LGSM AI G34/50-56 Lionikas (GBS)" + "EMSR", + "Ethanol-Medicated Stress Reduction", + "Family:Non-genetic Cohort" ], [ - "MDP", - "Mouse Diversity Panel (strain means)" + "B6D2", + "Glaucoma and Aged Retina UTHSC", + "Family:Non-genetic Cohort" ], [ "NZBXFVB-N2", - "NZB/FVB N2 NCI" + "NZB/FVB N2 NCI", + "Family:Non-genetic Cohort" ], [ "C57BL-6JxC57BL-6NJF2", - "Reduced Complexity Cross (B6JxB6N F2)" + "Reduced Complexity Cross (B6JxB6N F2)", + "Family:Non-genetic Cohort" ], [ "Retina-RGC-Rheaume", - "Retina RGC Rheaume" + "Retina RGC Rheaume", + "Family:Non-genetic Cohort" ], [ - "SOTNOT-OHSU", - "SOTNOT-OHSU" + "Scripps-2013", + "Scripps C57BL/6J", + "Family:Non-genetic Cohort" + ], + [ + "BXD300", + "BXD300", + "Family:None" ] ], "poplar": [ [ "Poplar", - "Poplar" + "Poplar", + "Family:None" ] ], "rat": [ [ "HXBBXH", - "HXB/BXH" - ], - [ - "HRDP", - "Hybrid Rat Diversity Panel" + "Hybrid Rat Diversity Panel (Includes HXB/BXH)", + "Family:None" ], [ "HSNIH-Palmer", - "NIH Heterogeneous Stock (Palmer)" + "NIH Heterogeneous Stock (Palmer)", + "Family:None" ], [ "HSNIH-RGSMC", - "NIH Heterogeneous Stock (RGSMC 2013)" + "NIH Heterogeneous Stock (RGSMC 2013)", + "Family:None" ], [ "SRxSHRSPF2", - "UIOWA SRxSHRSP F2" + "UIOWA SRxSHRSP F2", + "Family:None" ] ], "soybean": [ [ "J12XJ58F11", - "J12XJ58F11" + "J12XJ58F11", + "Family:None" ], [ "J12XJ58F2", - "J12XJ58F2" + "J12XJ58F2", + "Family:None" ] ], "tomato": [ [ "LXP", - "LXP" + "LXP", + "Family:None" ] ] }, @@ -4308,6 +5729,10 @@ "human", "Human (hg19)" ], + [ + "macaque monkey", + "Macaque monkey" + ], [ "mouse", "Mouse (mm10)" @@ -4480,6 +5905,10 @@ "Phenotypes", "Phenotypes" ], + [ + "Methylation", + "Methylation" + ], [ "Newborn Cord Blood mRNA", "Newborn Cord Blood mRNA" @@ -4493,12 +5922,206 @@ ], "GTEx": [ [ - "Adipose tissue, subcutaneous mRNA", - "Adipose tissue, subcutaneous mRNA" + "Adipose Tissue, Subcutaneous mRNA", + "Adipose Tissue, Subcutaneous mRNA" + ], + [ + "Adipose Tissue, Visceral mRNA", + "Adipose Tissue, Visceral mRNA" + ], + [ + "Adrenal Gland mRNA", + "Adrenal Gland mRNA" + ], + [ + "Amygdala mRNA", + "Amygdala mRNA" + ], + [ + "Anterior Cingulate Cortex mRNA", + "Anterior Cingulate Cortex mRNA" + ], + [ + "Aorta mRNA", + "Aorta mRNA" + ], + [ + "Blood, Cells - EBV-Transformed Lymphocytes mRNA", + "Blood, Cells - EBV-Transformed Lymphocytes mRNA" + ], + [ + "Breast - Mammary Tissue mRNA", + "Breast - Mammary Tissue mRNA" + ], + [ + "Caudate mRNA", + "Caudate mRNA" + ], + [ + "Cells - EBV-Transformed Lymphocytes mRNA", + "Cells - EBV-Transformed Lymphocytes mRNA" + ], + [ + "Cells - Leukemia Cell Line (CML) mRNA", + "Cells - Leukemia Cell Line (CML) mRNA" + ], + [ + "Cells - Transformed Fibroblasts mRNA", + "Cells - Transformed Fibroblasts mRNA" + ], + [ + "Cerebellar Cortex mRNA", + "Cerebellar Cortex mRNA" + ], + [ + "Cerebellar Hemisphere mRNA", + "Cerebellar Hemisphere mRNA" + ], + [ + "Cerebellum mRNA", + "Cerebellum mRNA" + ], + [ + "Colon - Transverse mRNA", + "Colon - Transverse mRNA" + ], + [ + "Coronary mRNA", + "Coronary mRNA" + ], + [ + "Esophagus - Mucosa mRNA", + "Esophagus - Mucosa mRNA" + ], + [ + "Esophagus - Muscularis mRNA", + "Esophagus - Muscularis mRNA" + ], + [ + "Fallopian Tube mRNA", + "Fallopian Tube mRNA" + ], + [ + "Frontal Cortex mRNA", + "Frontal Cortex mRNA" + ], + [ + "Heart - Atrial Appendage mRNA", + "Heart - Atrial Appendage mRNA" + ], + [ + "Heart - Left Ventricle mRNA", + "Heart - Left Ventricle mRNA" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Hypothalamus mRNA", + "Hypothalamus mRNA" + ], + [ + "Kidney mRNA", + "Kidney mRNA" + ], + [ + "Liver mRNA", + "Liver mRNA" + ], + [ + "Lung mRNA", + "Lung mRNA" + ], + [ + "Muscle mRNA", + "Muscle mRNA" + ], + [ + "Nerve - Tibial mRNA", + "Nerve - Tibial mRNA" + ], + [ + "Nucleus Accumbens mRNA", + "Nucleus Accumbens mRNA" + ], + [ + "Ovary mRNA", + "Ovary mRNA" + ], + [ + "Pancreas mRNA", + "Pancreas mRNA" + ], + [ + "Pituitary Gland mRNA", + "Pituitary Gland mRNA" + ], + [ + "Prostate mRNA", + "Prostate mRNA" + ], + [ + "Putamen mRNA", + "Putamen mRNA" + ], + [ + "Skin - Not Sun Exposed (Suprapubic) mRNA", + "Skin - Not Sun Exposed (Suprapubic) mRNA" + ], + [ + "Skin - Sun Exposed (Lower leg) mRNA", + "Skin - Sun Exposed (Lower leg) mRNA" + ], + [ + "Spinal Cord mRNA", + "Spinal Cord mRNA" + ], + [ + "Stomach mRNA", + "Stomach mRNA" + ], + [ + "Substantia Nigra mRNA", + "Substantia Nigra mRNA" + ], + [ + "Testis mRNA", + "Testis mRNA" + ], + [ + "Thyroid mRNA", + "Thyroid mRNA" + ], + [ + "Tibial mRNA", + "Tibial mRNA" + ], + [ + "Uterus mRNA", + "Uterus mRNA" + ], + [ + "Vagina mRNA", + "Vagina mRNA" + ], + [ + "Whole Blood mRNA", + "Whole Blood mRNA" + ] + ], + "GTEx_v5": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Adipose Tissue, Subcutaneous mRNA", + "Adipose Tissue, Subcutaneous mRNA" ], [ - "Adipose tissue, visceral mRNA", - "Adipose tissue, visceral mRNA" + "Adipose Tissue, Visceral mRNA", + "Adipose Tissue, Visceral mRNA" ], [ "Adrenal Gland mRNA", @@ -4517,8 +6140,12 @@ "Aorta mRNA" ], [ - "Blood, Cells - EBV-Transformed Lymphocytes mRNA", - "Blood, Cells - EBV-Transformed Lymphocytes mRNA" + "Bladder mRNA", + "Bladder mRNA" + ], + [ + "Bone Marrow mRNA", + "Bone Marrow mRNA" ], [ "Breast - Mammary Tissue mRNA", @@ -4532,10 +6159,6 @@ "Cells - EBV-Transformed Lymphocytes mRNA", "Cells - EBV-Transformed Lymphocytes mRNA" ], - [ - "Cells - Leukemia Cell Line (CML) mRNA", - "Cells - Leukemia Cell Line (CML) mRNA" - ], [ "Cells - Transformed Fibroblasts mRNA", "Cells - Transformed Fibroblasts mRNA" @@ -4552,6 +6175,14 @@ "Cerebellum mRNA", "Cerebellum mRNA" ], + [ + "Cervix mRNA", + "Cervix mRNA" + ], + [ + "Colon - Sigmoid mRNA", + "Colon - Sigmoid mRNA" + ], [ "Colon - Transverse mRNA", "Colon - Transverse mRNA" @@ -4560,6 +6191,10 @@ "Coronary mRNA", "Coronary mRNA" ], + [ + "Esophagus - Gastroesophageal mRNA", + "Esophagus - Gastroesophageal mRNA" + ], [ "Esophagus - Mucosa mRNA", "Esophagus - Mucosa mRNA" @@ -4636,6 +6271,10 @@ "Putamen mRNA", "Putamen mRNA" ], + [ + "Salivary Gland mRNA", + "Salivary Gland mRNA" + ], [ "Skin - Not Sun Exposed (Suprapubic) mRNA", "Skin - Not Sun Exposed (Suprapubic) mRNA" @@ -4644,10 +6283,18 @@ "Skin - Sun Exposed (Lower leg) mRNA", "Skin - Sun Exposed (Lower leg) mRNA" ], + [ + "Small Intestine - Terminal Ileum mRNA", + "Small Intestine - Terminal Ileum mRNA" + ], [ "Spinal Cord mRNA", "Spinal Cord mRNA" ], + [ + "Spleen mRNA", + "Spleen mRNA" + ], [ "Stomach mRNA", "Stomach mRNA" @@ -4681,18 +6328,18 @@ "Whole Blood mRNA" ] ], - "GTEx_v5": [ + "GTEx_v8": [ [ "Phenotypes", "Phenotypes" ], [ - "Adipose tissue, subcutaneous mRNA", - "Adipose tissue, subcutaneous mRNA" + "Adipose Tissue, Subcutaneous mRNA", + "Adipose Tissue, Subcutaneous mRNA" ], [ - "Adipose tissue, visceral mRNA", - "Adipose tissue, visceral mRNA" + "Adipose Tissue, Visceral mRNA", + "Adipose Tissue, Visceral mRNA" ], [ "Adrenal Gland mRNA", @@ -4710,14 +6357,6 @@ "Aorta mRNA", "Aorta mRNA" ], - [ - "Bladder mRNA", - "Bladder mRNA" - ], - [ - "Bone Marrow mRNA", - "Bone Marrow mRNA" - ], [ "Breast - Mammary Tissue mRNA", "Breast - Mammary Tissue mRNA" @@ -4746,10 +6385,6 @@ "Cerebellum mRNA", "Cerebellum mRNA" ], - [ - "Cervix mRNA", - "Cervix mRNA" - ], [ "Colon - Sigmoid mRNA", "Colon - Sigmoid mRNA" @@ -4774,10 +6409,6 @@ "Esophagus - Muscularis mRNA", "Esophagus - Muscularis mRNA" ], - [ - "Fallopian Tube mRNA", - "Fallopian Tube mRNA" - ], [ "Frontal Cortex mRNA", "Frontal Cortex mRNA" @@ -5009,6 +6640,10 @@ [ "Phenotypes", "Phenotypes" + ], + [ + "Islets mRNA", + "Islets mRNA" ] ], "TIGEM-Retina-RNA-Seq": [ @@ -5022,53 +6657,31 @@ ] ] }, - "mouse": { - "AIL": [ + "macaque monkey": { + "Macaca-fasicularis": [ [ - "Phenotypes", - "Phenotypes" + "Amygdala mRNA", + "Amygdala mRNA" ], [ - "Genotypes", - "Genotypes" + "Brain mRNA", + "Brain mRNA" ], [ "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA" + "Nucleus Accumbens mRNA", + "Nucleus Accumbens mRNA" ], [ - "Striatum mRNA", - "Striatum mRNA" - ] - ], - "AIL-LGSM-F34-A": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], - "AIL-LGSM-F34-F39-43-GBS": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], - "AIL-LGSM-F34-GBS": [ - [ - "Phenotypes", - "Phenotypes" - ] - ], - "AIL-LGSM-F39-43-GBS": [ - [ - "Phenotypes", - "Phenotypes" + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" ] - ], + ] + }, + "mouse": { "AKXD": [ [ "Genotypes", @@ -5105,6 +6718,16 @@ "Liver mRNA" ] ], + "B6-Lens": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Ocular Lens mRNA", + "Ocular Lens mRNA" + ] + ], "B6BTBRF2": [ [ "Phenotypes", @@ -5123,6 +6746,14 @@ [ "Phenotypes", "Phenotypes" + ], + [ + "Retina microRNA", + "Retina microRNA" + ], + [ + "Retina mRNA", + "Retina mRNA" ] ], "B6D2F2": [ @@ -5143,6 +6774,10 @@ [ "Genotypes", "Genotypes" + ], + [ + "Muscle mRNA", + "Muscle mRNA" ] ], "B6D2RI": [ @@ -5195,6 +6830,10 @@ [ "Liver mRNA", "Liver mRNA" + ], + [ + "Muscle mRNA", + "Muscle mRNA" ] ], "BHHBF2": [ @@ -5284,6 +6923,10 @@ "Hippocampal Precursor Cells mRNA", "Hippocampal Precursor Cells mRNA" ], + [ + "Hippocampus microRNA", + "Hippocampus microRNA" + ], [ "Hippocampus mRNA", "Hippocampus mRNA" @@ -5296,6 +6939,14 @@ "Kidney mRNA", "Kidney mRNA" ], + [ + "Leucocytes mRNA", + "Leucocytes mRNA" + ], + [ + "Liver DNAm", + "Liver DNAm" + ], [ "Liver Metabolome", "Liver Metabolome" @@ -5316,6 +6967,10 @@ "Midbrain mRNA", "Midbrain mRNA" ], + [ + "Muscle Metabolome", + "Muscle Metabolome" + ], [ "Muscle mRNA", "Muscle mRNA" @@ -5324,6 +6979,10 @@ "Neocortex mRNA", "Neocortex mRNA" ], + [ + "Neutrophils mRNA", + "Neutrophils mRNA" + ], [ "Nucleus Accumbens mRNA", "Nucleus Accumbens mRNA" @@ -5332,6 +6991,10 @@ "Pituitary Gland mRNA", "Pituitary Gland mRNA" ], + [ + "Popliteal Lymph Node mRNA", + "Popliteal Lymph Node mRNA" + ], [ "Prefrontal Cortex mRNA", "Prefrontal Cortex mRNA" @@ -5356,6 +7019,10 @@ "T Cell (regulatory) mRNA", "T Cell (regulatory) mRNA" ], + [ + "Thymus mRNA", + "Thymus mRNA" + ], [ "Ventral Tegmental Area mRNA", "Ventral Tegmental Area mRNA" @@ -5377,12 +7044,20 @@ "Genotypes" ], [ - "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus Proteome", + "Hippocampus Proteome" + ], + [ + "Liver DNAm", + "Liver DNAm" ], [ "Liver mRNA", "Liver mRNA" + ], + [ + "Liver Proteome", + "Liver Proteome" ] ], "BXD300": [ @@ -5431,6 +7106,20 @@ "Genotypes" ] ], + "CC": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Midbrain mRNA", + "Midbrain mRNA" + ] + ], "CFW": [ [ "Phenotypes", @@ -5471,12 +7160,24 @@ [ "Midbrain mRNA", "Midbrain mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ], + [ + "Striatum mRNA", + "Striatum mRNA" ] ], "CMS": [ [ "Phenotypes", "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" ] ], "CTB6F2": [ @@ -5541,6 +7242,32 @@ "Retina mRNA" ] ], + "DOD-BXD-GWI": [ + [ + "Genotypes", + "Genotypes" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ] + ], + "EMSR": [ + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ] + ], + "HET3-ITP": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], "HS": [ [ "Phenotypes", @@ -5565,6 +7292,54 @@ "Striatum mRNA" ] ], + "JAX-D2-Mono-RNA-Seq": [ + [ + "Retina mRNA", + "Retina mRNA" + ] + ], + "LGSM-AI": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ], + [ + "Striatum mRNA", + "Striatum mRNA" + ] + ], + "LGSM-AI-G34-A": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "LGSM-AI-G34-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "LGSM-AI-G34_39-43-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "LGSM-AI-G39-43-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "LGSM-AIG34_50-56-GBS": [ [ "Phenotypes", @@ -5580,6 +7355,10 @@ "Genotypes", "Genotypes" ], + [ + "Brain mRNA", + "Brain mRNA" + ], [ "Hippocampus mRNA", "Hippocampus mRNA" @@ -5654,6 +7433,22 @@ "Genotypes", "Genotypes" ] + ], + "Scripps-2013": [ + [ + "Anterior Cingulate Cortex mRNA", + "Anterior Cingulate Cortex mRNA" + ] + ], + "UTHSC-Cannabinoid": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] ] }, "poplar": { @@ -5665,16 +7460,6 @@ ] }, "rat": { - "HRDP": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ] - ], "HSNIH-Palmer": [ [ "Phenotypes", -- cgit v1.2.3 From 75ecdb25c7a598f0f254f4f53529b657736aaa49 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 27 Apr 2020 14:00:34 -0500 Subject: Made change that should allow dataset structure to be loaded from Redis instead of the JSON file without breaking things --- wqflask/base/data_set.py | 41 +++++++++++++--------- wqflask/wqflask/__init__.py | 4 +-- wqflask/wqflask/api/gen_menu.py | 18 ---------- wqflask/wqflask/collect.py | 2 +- .../new/javascript/dataset_select_menu_orig.js | 1 + 5 files changed, 28 insertions(+), 38 deletions(-) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1f99df49..fd1dff5c 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -93,22 +93,26 @@ Publish or ProbeSet. E.g. """ self.datasets = {} - data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) - #data = gen_menu.gen_dropdown_json() - - - for species in data['datasets']: - for group in data['datasets'][species]: - for dataset_type in data['datasets'][species][group]: - for dataset in data['datasets'][species][group][dataset_type]: - short_dataset_name = dataset[1] - if dataset_type == "Phenotypes": - new_type = "Publish" - elif dataset_type == "Genotypes": - new_type = "Geno" - else: - new_type = "ProbeSet" - self.datasets[short_dataset_name] = new_type + + data = Redis.get("dataset_structure") + if data: + self.datasets = json.loads(data) + else: #ZS: I don't think this should ever run unless Redis is emptied + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) + for species in data['datasets']: + for group in data['datasets'][species]: + for dataset_type in data['datasets'][species][group]: + for dataset in data['datasets'][species][group][dataset_type]: + short_dataset_name = dataset[1] + if dataset_type == "Phenotypes": + new_type = "Publish" + elif dataset_type == "Genotypes": + new_type = "Geno" + else: + new_type = "ProbeSet" + self.datasets[short_dataset_name] = new_type + + Redis.set("dataset_structure", json.dumps(self.datasets)) # Set LOG_LEVEL_DEBUG=5 to see the following: logger.debugf(5, "datasets",self.datasets) @@ -127,6 +131,7 @@ Publish or ProbeSet. E.g. results = g.db.execute(geno_query).fetchall() if len(results): self.datasets[name] = "ProbeSet" + Redis.set("dataset_structure", json.dumps(self.datasets)) return self.datasets[name] group_name = name.replace("Publish", "") @@ -140,6 +145,7 @@ Publish or ProbeSet. E.g. results = g.db.execute(pheno_query).fetchall() if len(results): self.datasets[name] = "Publish" + Redis.set("dataset_structure", json.dumps(self.datasets)) return self.datasets[name] #ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary @@ -151,6 +157,7 @@ Publish or ProbeSet. E.g. results = g.db.execute(other_pheno_query).fetchall() if len(results): self.datasets[name] = "Publish" + Redis.set("dataset_structure", json.dumps(self.datasets)) return self.datasets[name] geno_query = """ @@ -166,11 +173,11 @@ Publish or ProbeSet. E.g. results = g.db.execute(geno_query).fetchall() if len(results): self.datasets[name] = "Geno" + Redis.set("dataset_structure", json.dumps(self.datasets)) return self.datasets[name] #ZS: It shouldn't ever reach this return None - else: return self.datasets[name] diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 399e794d..62e98b36 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -21,5 +21,5 @@ app.jinja_env.globals.update( numify = formatting.numify ) -import wqflask.views -from wqflask.api import router \ No newline at end of file +from wqflask.api import router +import wqflask.views \ No newline at end of file diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index adf66fb5..c7bcb65d 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -1,7 +1,6 @@ from __future__ import print_function, division import sys -import json from flask import g @@ -23,14 +22,6 @@ def gen_dropdown_json(): types = get_types(groups) datasets = get_datasets(types) - #species.append(('All Species', 'All Species')) - #groups['All Species'] = [('All Groups', 'All Groups')] - #types['All Species'] = {} - #types['All Species']['All Groups'] = [('Phenotypes', 'Phenotypes')] - #datasets['All Species'] = {} - #datasets['All Species']['All Groups'] = {} - #datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')] - data = dict(species=species, groups=groups, types=types, @@ -55,15 +46,6 @@ def get_groups(species): groups = {} for species_name, _species_full_name in species: groups[species_name] = [] - # results = g.db.execute("""SELECT InbredSet.Name, InbredSet.FullName - # FROM InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze - # WHERE Species.Name = '{}' AND - # InbredSet.SpeciesId = Species.Id AND - # (PublishFreeze.InbredSetId = InbredSet.Id OR - # GenoFreeze.InbredSetId = InbredSet.Id OR - # ProbeFreeze.InbredSetId = InbredSet.Id) - # GROUP by InbredSet.Name - # ORDER BY InbredSet.FullName""".format(species_name)).fetchall() results = g.db.execute("""SELECT InbredSet.Name, InbredSet.FullName, IFNULL(InbredSet.Family, 'None') FROM InbredSet, Species diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 1d74b699..b22e0004 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -185,7 +185,7 @@ def delete_collection(): if len(uc_id.split(":")) > 1: flash("We've deleted the selected collections.", "alert-info") else: - flash("We've deleted the collection: {}.".format(uc_id), "alert-info") + flash("We've deleted the selected collection.", "alert-info") else: flash("We've deleted the collection: {}.".format(collection_name), "alert-info") diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js index 794804f4..ee7be68c 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -6,6 +6,7 @@ process_json = function(data) { return apply_default(); } }; + $.ajax('/api/v_pre1/gen_dropdown', { dataType: 'json', success: process_json -- cgit v1.2.3 From caa9966df61a9e4290d36af557adc3ede1a3674b Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 27 Apr 2020 14:08:30 -0500 Subject: Added timeout for when/if it does the REST API query, so it doesn't hang indefinitely --- wqflask/base/data_set.py | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index fd1dff5c..cab708ef 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -98,19 +98,22 @@ Publish or ProbeSet. E.g. if data: self.datasets = json.loads(data) else: #ZS: I don't think this should ever run unless Redis is emptied - data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) - for species in data['datasets']: - for group in data['datasets'][species]: - for dataset_type in data['datasets'][species][group]: - for dataset in data['datasets'][species][group][dataset_type]: - short_dataset_name = dataset[1] - if dataset_type == "Phenotypes": - new_type = "Publish" - elif dataset_type == "Genotypes": - new_type = "Geno" - else: - new_type = "ProbeSet" - self.datasets[short_dataset_name] = new_type + try: + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout = 5).content) + for species in data['datasets']: + for group in data['datasets'][species]: + for dataset_type in data['datasets'][species][group]: + for dataset in data['datasets'][species][group][dataset_type]: + short_dataset_name = dataset[1] + if dataset_type == "Phenotypes": + new_type = "Publish" + elif dataset_type == "Genotypes": + new_type = "Geno" + else: + new_type = "ProbeSet" + self.datasets[short_dataset_name] = new_type + except: + pass Redis.set("dataset_structure", json.dumps(self.datasets)) -- cgit v1.2.3