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authorZachary Sloan2012-09-06 17:21:11 -0500
committerZachary Sloan2012-09-06 17:21:11 -0500
commitc599ccf86e8db0f031007937dbdfe0da4b0e56e7 (patch)
tree266d3859e525ff1d65c84ee6839efe7f1cae111a
parent378ba76a93c07dfc5be6c745a2216e24aa0f83da (diff)
downloadgenenetwork2-c599ccf86e8db0f031007937dbdfe0da4b0e56e7.tar.gz
Put the correlation tool options into the template and wrote some coffee script to automatically change the description text below.
-rwxr-xr-xwqflask/wqflask/show_trait/DataEditingPage.py53
-rw-r--r--wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee22
-rw-r--r--wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js19
-rw-r--r--wqflask/wqflask/templates/trait_data_and_analysis.html2019
4 files changed, 172 insertions, 1941 deletions
diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index affcd449..d619f26c 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -232,17 +232,31 @@ class DataEditingPage(templatePage):
# - Interquartile Range
# """)
- self.basic_table['columns'] = yaml.load("""
- -
- n: All Cases
- t: all
- -
- n: BXD Only
- t: primary
- -
- n: Non-BXD Only
- t: other
- """)
+ #self.sample_groups = []
+ #self.sample_groups.append(dict(label=fd.RISet + " Only",
+ # value="primary_only"))
+ #self.sample_groups.append(dict(label="Non-"+fd.RISet,
+ # value="other_only"))
+ #self.sample_groups.append(dict(label="All Cases",
+ # value="all_cases"))
+
+ self.sample_groups = OrderedDict()
+ self.sample_groups['primary_only'] = fd.RISet + " Only"
+ self.sample_groups['other_only'] = "Non-" + fd.RISet
+ self.sample_groups['all_cases'] = "All Cases"
+
+
+ #self.basic_table['columns'] = yaml.load("""
+ # -
+ # n: All Cases
+ # t: all
+ # -
+ # n: BXD Only
+ # t: primary
+ # -
+ # n: Non-BXD Only
+ # t: other
+ # """)
print(pf(self.basic_table))
@@ -1160,7 +1174,7 @@ class DataEditingPage(templatePage):
(RISetgp, webqtlConfig.PUBLICTHRESH))
for item in self.cursor.fetchall():
dataset_menu.append(dict(tissue=None,
- datasets=item))
+ datasets=[item]))
self.cursor.execute('''SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,
InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name =
@@ -1168,7 +1182,7 @@ class DataEditingPage(templatePage):
(RISetgp, webqtlConfig.PUBLICTHRESH))
for item in self.cursor.fetchall():
dataset_menu.append(dict(tissue=None,
- datasets=item))
+ datasets=[item]))
#03/09/2009: Xiaodong changed the SQL query to order by Name as requested by Rob.
self.cursor.execute('SELECT Id, Name FROM Tissue order by Name')
@@ -1195,16 +1209,14 @@ class DataEditingPage(templatePage):
dataset_menu_selected = None
if len(dataset_menu):
if thisTrait and thisTrait.db:
- dataset_menu_selected = thisTrait.db.fullname
+ dataset_menu_selected = thisTrait.db.name
#criteriaText = HT.Span("Return:", Class="ffl fwb fs12")
#criteriaMenu1 = HT.Select(name='criteria1', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);")
- return_results_menu = []
-
- for counter in (100, 200, 500, 1000, 2000, 5000, 10000, 15000, 20000):
- return_results_menu.append(('top %s' % (counter,), str(counter)))
+ return_results_menu = (100, 200, 500, 1000, 2000, 5000, 10000, 15000, 20000)
+ return_results_menu_selected = 500
#criteriaMenu1.append(('top 100','100'))
#criteriaMenu1.append(('top 200','200'))
@@ -1334,9 +1346,10 @@ class DataEditingPage(templatePage):
#submitTable.append(corr_script)
#
#title3Body.append(submitTable)
- self.correlation_tools = dict(dataset_menu = dataset_menu,
+ self.corr_tools = dict(dataset_menu = dataset_menu,
dataset_menu_selected = dataset_menu_selected,
- return_results_menu = return_results_menu)
+ return_results_menu = return_results_menu,
+ return_results_menu_selected = return_results_menu_selected,)
def dispMappingTools(self, fd, title4Body, thisTrait):
diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
index 77415d32..f13dc5bf 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
@@ -11,7 +11,6 @@ $ ->
hide_tabs(1)
-
# Changes stats table between all, bxd only and non-bxd, etc.
stats_mdp_change = ->
selected = $(this).val()
@@ -20,7 +19,6 @@ $ ->
$(".stats_mdp").change(stats_mdp_change)
-
update_stat_values = (the_values)->
for category in ['primary', 'other', 'all']
id = "#" + process_id(category, "mean")
@@ -153,7 +151,25 @@ $ ->
console.log("Found Show Outliers")
$('#show_hide_outliers').val("Hide Outliers")
console.log("Should be now Hide Outliers")
-
+
+ ###
+ Calculate Correlations Code
+ ###
+
+ on_corr_method_change = ->
+ console.log("in beginning of on_corr_method_change")
+ corr_method = $('select[name=corr_method]').val()
+ console.log("corr_method is:", corr_method)
+ $('.correlation_desc').hide()
+ $('#' + corr_method + "_r_desc").show().effect("highlight")
+
+ $('select[name=corr_method]').change(on_corr_method_change)
+
+ ###
+ End Calculate Correlations Code
+ ###
+
+
console.log("before registering show_hide_outliers")
$('#show_hide_outliers').click(show_hide_outliers)
console.log("after registering show_hide_outliers")
diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
index 6357a7da..96b245ea 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
@@ -10,7 +10,7 @@
};
$(function() {
- var edit_data_change, hide_tabs, make_table, process_id, show_hide_outliers, stats_mdp_change, update_stat_values;
+ var edit_data_change, hide_tabs, make_table, on_corr_method_change, process_id, show_hide_outliers, stats_mdp_change, update_stat_values;
hide_tabs = function(start) {
var x, _i, _results;
_results = [];
@@ -186,6 +186,23 @@
return console.log("Should be now Hide Outliers");
}
};
+ /*
+ Calculate Correlations Code
+ */
+
+ on_corr_method_change = function() {
+ var corr_method;
+ console.log("in beginning of on_corr_method_change");
+ corr_method = $('select[name=corr_method]').val();
+ console.log("corr_method is:", corr_method);
+ $('.correlation_desc').hide();
+ return $('#' + corr_method + "_r_desc").show().effect("highlight");
+ };
+ $('select[name=corr_method]').change(on_corr_method_change);
+ /*
+ End Calculate Correlations Code
+ */
+
console.log("before registering show_hide_outliers");
$('#show_hide_outliers').click(show_hide_outliers);
console.log("after registering show_hide_outliers");
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index 3644b436..f6917a90 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -10,14 +10,14 @@
<td valign="top" width="100%" bgcolor="#FAFAFA">
<form method="post" action="/webqtl/main.py" name="dataInput"></form>
{# <input type="hidden" name="isSE" value="yes">
- <input type="hidden" name="permCheck">
- <input type="hidden" name="otherStrainVals" value="_">
+ <input type="hidden" name="permCheck">
+ <input type="hidden" name="otherStrainVals" value="_">
<input type="hidden" name="FormID" value="dataEditing">
- <input type="hidden" name="normalPlotTitle" value="Sall3: 1441186_at">
- <input type="hidden" name="strainVars" value="_">
- <input type="hidden" name="additiveCheck" value="ON">
- <input type="hidden" name="incparentsf1" value="ON">
- <input type="hidden" name="strainNames" value="_">
+ <input type="hidden" name="normalPlotTitle" value="Sall3: 1441186_at">
+ <input type="hidden" name="strainVars" value="_">
+ <input type="hidden" name="additiveCheck" value="ON">
+ <input type="hidden" name="incparentsf1" value="ON">
+ <input type="hidden" name="strainNames" value="_">
<input type="hidden" name="submitID" value="">
<input type="hidden" name="scale" value="physic">
<input type="hidden" name="intervalAnalystCheck" value="ON">
@@ -240,13 +240,15 @@
<p class="sectionheader" id="title2" style="border-radius: 5px;">&nbsp;&nbsp;Basic Statistics</p>
- <p id="sectionbody2"></p>Include: <select name="stats_mdp" size="1" class="stats_mdp">
- {% for mdp in MDP_menu %}
- <option value="{{ mdp[1] }}">
- {{ mdp[0] }}
- </option>
- {% endfor %}
- </select><br>
+
+ <p id="sectionbody2"></p>Include:
+ <select name="corr_samples_group" size="1">
+ {% for group, pretty_group in sample_groups.items() %}
+ <option value="{{ group }}">
+ {{ pretty_group }}
+ </option>
+ {% endfor %}
+ </select><br>
<br>
<input type="button" name="Default_Name" class="button update" value=" Update Figures "><br>
<br>
@@ -693,14 +695,6 @@
<tr>
<td>
<div class="ui-tabs" id="corr_tabs">
- <ul>
- <li><a href="#corrtabs-1">Sample r</a></li>
-
- <li><a href="#corrtabs-2">Literature r</a></li>
-
- <li><a href="#corrtabs-3">Tissue r</a></li>
- </ul>
-
<div id="corrtabs-1">
<table cellpadding="0" cellspacing="0" width="100%">
<tr>
@@ -709,1914 +703,105 @@
<table cellpadding="2" cellspacing="0" width="619px">
<tr>
- <td><span class="ffl fwb fs12">Database:</span></td>
-
- <td colspan="3"><select name="database1" size="1">
- <option value="BXDPublish">
- BXD Published Phenotypes
- </option>
-
- <option value="BXDGeno">
- BXD Genotypes
- </option>
-
- <optgroup label="Amygdala ------">
- <option value="INIA_AmgCoh_0311">
- INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA
- </option>
-
- <option value="INIA_Amg_BLA_RMA_1110">
- INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA
- </option>
-
- <option value="INIA_Amg_BLA_RMA_M_1110">
- INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Male
- </option>
-
- <option value="INIA_Amg_BLA_RMA_F_1110">
- INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female
- </option>
- </optgroup>
-
- <optgroup label="Brain ------">
- <option value="BR_M2_1106_R">
- UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA
- </option>
-
- <option value="IBR_M_0606_R">
- INIA Brain mRNA M430 (Jun06) RMA
- </option>
-
- <option value="IBR_M_0106_P">
- INIA Brain mRNA M430 (Jan06) PDNN
- </option>
-
- <option value="IBR_M_0106_R">
- INIA Brain mRNA M430 (Jan06) RMA
- </option>
-
- <option value="BR_U_1105_P">
- UTHSC Brain mRNA U74Av2 (Nov05) PDNN
- </option>
-
- <option value="BR_U_0805_R">
- UTHSC Brain mRNA U74Av2 (Aug05) RMA
- </option>
-
- <option value="BR_U_0805_P">
- UTHSC Brain mRNA U74Av2 (Aug05) PDNN
- </option>
-
- <option value="BR_U_0805_M">
- UTHSC Brain mRNA U74Av2 (Aug05) MAS5
- </option>
-
- <option value="CB_M_0204_P">
- INIA Brain mRNA M430 (Feb04) PDNN
- </option>
- </optgroup>
-
- <optgroup label="Cartilage ------">
- <option value="UCLA_BXDBXH_CARTILAGE_V2">
- UCLA BXD and BXH Cartilage v2
- </option>
-
- <option value="UCLA_BXDBXH_CARTILAGE">
- UCLA BXD and BXH Cartilage
- </option>
-
- <option value="UCLA_BXD_CARTILAGE">
- UCLA BXD Cartilage
- </option>
- </optgroup>
-
- <optgroup label="Cerebellum ------">
- <option value="GCB_M2_0505_M">
- GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5
- </option>
-
- <option value="GCB_M2_0505_P">
- GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN
- </option>
-
- <option value="GCB_M2_0505_R">
- GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA
- </option>
-
- <option value="CB_M_0305_M">
- SJUT Cerebellum mRNA M430 (Mar05) MAS5
- </option>
-
- <option value="CB_M_0305_P">
- SJUT Cerebellum mRNA M430 (Mar05) PDNN
- </option>
-
- <option value="CB_M_0305_R">
- SJUT Cerebellum mRNA M430 (Mar05) RMA
- </option>
-
- <option value="CB_M_1004_M">
- SJUT Cerebellum mRNA M430 (Oct04) MAS5
- </option>
-
- <option value="CB_M_1004_P">
- SJUT Cerebellum mRNA M430 (Oct04) PDNN
- </option>
-
- <option value="CB_M_1004_R">
- SJUT Cerebellum mRNA M430 (Oct04) RMA
- </option>
-
- <option value="CB_M_1003_M">
- SJUT Cerebellum mRNA M430 (Oct03) MAS5
- </option>
- </optgroup>
-
- <optgroup label="Eye ------">
- <option value="Eye_M2_0908_R">
- Eye M430v2 (Sep08) RMA
- </option>
-
- <option value="Eye_M2_0908_R_NB">
- Eye M430v2 Mutant Gpnmb (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_R_ND">
- Eye M430v2 WT Gpnmb (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_R_MT">
- Eye M430v2 Mutant Tyrp1 (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_WTWT">
- Eye M430v2 WT WT (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_R_WT">
- Eye M430v2 WT Tyrp1 (Sep08) RMA **
- </option>
-
- <option value="BXD_GLA_0911">
- BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **
- </option>
- </optgroup>
-
- <optgroup label="Hematopoietic Cells ------">
- <option value="UMCG_0907_HemaStem_ori">
- UMCG Stem Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_HemaStem">
- UMCG Stem Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="UMCG_0907_Pro_ori">
- UMCG Progenitor Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_Pro">
- UMCG Progenitor Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="UMCG_0907_Eryth_ori">
- UMCG Erythroid Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_Eryth">
- UMCG Erythroid Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="UMCG_0907_Myeloid_ori">
- UMCG Myeloid Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_Myeloid">
- UMCG Myeloid Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="HC_U_0304_R">
- GNF Stem Cells U74Av2 (Mar04) RMA
- </option>
- </optgroup>
-
- <optgroup label="Hippocampus ------">
- <option value="HC_M2_0606_P" selected>
- Hippocampus Consortium M430v2 (Jun06) PDNN
- </option>
-
- <option value="HC_M2_0606_M">
- Hippocampus Consortium M430v2 (Jun06) MAS5
- </option>
-
- <option value="HC_M2_0606_R">
- Hippocampus Consortium M430v2 (Jun06) RMA
- </option>
-
- <option value="UMUTAffyExon_0209_RMA">
- UMUTAffy Hippocampus Exon (Feb09) RMA
- </option>
-
- <option value="UT_ILM_BXD_hipp_NON_0909">
- UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_NOS_0909">
- UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_NOE_0909">
- UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_RSS_0909">
- UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_RSE_0909">
- UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv
- </option>
- </optgroup>
-
- <optgroup label="Hypothalamus ------">
- <option value="INIA_Hyp_RMA_1110">
- INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)
- </option>
-
- <option value="INIA_Hyp_M_RMA_1110">
- INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Male
- </option>
-
- <option value="INIA_Hyp_F_RMA_1110">
- INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Female
- </option>
- </optgroup>
-
- <optgroup label="Kidney ------">
- <option value="MA_M2F_0706_R">
- Mouse kidney M430v2 Female (Aug06) RMA
- </option>
-
- <option value="MA_M2M_0706_R">
- Mouse kidney M430v2 Male (Aug06) RMA
- </option>
-
- <option value="MA_M2_0806_R">
- Mouse kidney M430v2 Sex Balanced (Aug06) RMA
- </option>
-
- <option value="MA_M2_0806_P">
- Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN
- </option>
-
- <option value="MA_M2_0706_P">
- Mouse Kidney M430v2 (Jul06) PDNN
- </option>
-
- <option value="MA_M2_0706_R">
- Mouse Kidney M430v2 (Jul06) RMA
- </option>
- </optgroup>
-
- <optgroup label="Leucocytes ------">
- <option value="Illum_BXD_PBL_1108">
- UWA Illumina PBL (Nov08) RSN **
- </option>
- </optgroup>
-
- <optgroup label="Liver ------">
- <option value="GSE16780_UCLA_ML0911">
- GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA
- </option>
-
- <option value="LV_G_0106_F">
- UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females
- </option>
-
- <option value="LV_G_0106_M">
- UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males
- </option>
-
- <option value="LV_G_0106_B">
- UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes
- </option>
-
- <option value="GenEx_BXD_liverSal_RMA_F_0211">
- GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **
- </option>
-
- <option value="GenEx_BXD_liverSal_RMA_M_0211">
- GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **
- </option>
-
- <option value="GenEx_BXD_liverSal_RMA_0211">
- GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **
- </option>
-
- <option value="GenEx_BXD_liverEt_RMA_F_0211">
- GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **
- </option>
-
- <option value="GenEx_BXD_liverEt_RMA_M_0211">
- GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **
- </option>
-
- <option value="GenEx_BXD_liverEt_RMA_0211">
- GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **
- </option>
-
- <option value="SUH_Liv_RMA_0611">
- SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **
- </option>
- </optgroup>
-
- <optgroup label="Lung ------">
- <option value="HZI_0408_R">
- HZI Lung M430v2 (Apr08) RMA
- </option>
-
- <option value="HZI_0408_M">
- HZI Lung M430v2 (Apr08) MAS5
- </option>
- </optgroup>
-
- <optgroup label="Midbrain ------">
- <option value="VUBXDMouseMidBrainQ0512">
- VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile **
- </option>
- </optgroup>
-
- <optgroup label="Muscle ------">
- <option value="EPFLMouseMuscleRMA1211">
- EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **
- </option>
-
- <option value="EPFLMouseMuscleHFDRMA1211">
- EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **
- </option>
-
- <option value="EPFLMouseMuscleCDRMA1211">
- EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **
- </option>
- </optgroup>
-
- <optgroup label="Neocortex ------">
- <option value="DevNeocortex_ILM6.2P14RInv_1111">
- BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv
- </option>
-
- <option value="DevNeocortex_ILM6.2P3RInv_1111">
- BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv
- </option>
-
- <option value="HQFNeoc_1210v2_RankInv">
- HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv
- </option>
-
- <option value="HQFNeoc_1210_RankInv">
- HQF BXD Neocortex ILM6v1.1 (Dec10) RankInv
- </option>
-
- <option value="HQFNeoc_0208_RankInv">
- HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv
- </option>
-
- <option value="DevNeocortex_ILM6.2P14RInv_1110">
- BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv
- </option>
-
- <option value="DevNeocortex_ILM6.2P3RInv_1110">
- BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv
- </option>
- </optgroup>
-
- <optgroup label="Nucleus Accumbens ------">
- <option value="VCUSalo_1007_R">
- VCU BXD NA Sal M430 2.0 (Oct07) RMA
- </option>
-
- <option value="VCUEtOH_1007_R">
- VCU BXD NA EtOH M430 2.0 (Oct07) RMA **
- </option>
-
- <option value="VCUSal_1007_R">
- VCU BXD NA Et vs Sal M430 2.0 (Oct07) Sscore **
- </option>
- </optgroup>
-
- <optgroup label="Prefrontal Cortex ------">
- <option value="VCUEtOH_1206_R">
- VCU BXD PFC EtOH M430 2.0 (Dec06) RMA
- </option>
-
- <option value="VCUSal_1206_R">
- VCU BXD PFC Sal M430 2.0 (Dec06) RMA
- </option>
-
- <option value="VCUSal_1006_R">
- VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore
- </option>
-
- <option value="VCU_PF_Air_0111_R">
- VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **
- </option>
-
- <option value="VCU_PF_Et_0111_R">
- VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **
- </option>
-
- <option value="VCU_PF_AvE_0111_Ss">
- VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **
- </option>
- </optgroup>
-
- <optgroup label="Retina ------">
- <option value="G2NEI_ILM_Retina_BXD_RI0410">
- Normal HEI Retina (April 2010) RankInv
- </option>
-
- <option value="Illum_Retina_BXD_RankInv0410">
- Full HEI Retina (April 2010) RankInv
- </option>
-
- <option value="ONCRetILM6_0412">
- ONC HEI Retina (April 2012) RankInv
- </option>
-
- <option value="B6D2ONCILM_0412">
- B6D2 ONC Retina (April 2012) RankInv **
- </option>
-
- <option value="G2HEIONCRetILM6_0911">
- G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **
- </option>
-
- <option value="HEIONCvsCRetILM6_0911">
- HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **
- </option>
- </optgroup>
-
- <optgroup label="Spleen ------">
- <option value="UTHSC_SPL_RMA_1210">
- UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA
- </option>
-
- <option value="UTHSC_SPL_RMA_1010">
- UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA
- </option>
-
- <option value="IoP_SPL_RMA_0509">
- IoP Affy MOE 430v2 Spleen (May09) RMA
- </option>
-
- <option value="Illum_BXD_Spl_1108">
- UWA Illumina Spleen (Nov08) RSN **
- </option>
-
- <option value="UTK_BXDSpl_VST_0110">
- UTK Spleen ILM6.1 (Jan10) VST
- </option>
- </optgroup>
-
- <optgroup label="Striatum ------">
- <option value="DevStriatum_ILM6.2P14RInv_1111">
- BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **
- </option>
-
- <option value="DevStriatum_ILM6.2P3RInv_1111">
- BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **
- </option>
-
- <option value="UTHSC_Striatum_RankInv_1210">
- HQF BXD Striatum ILM6.1 (Dec10v2) RankInv
- </option>
-
- <option value="UTHSC_Str_RankInv_1210">
- HQF BXD Striatum ILM6.1 (Dec10) RankInv
- </option>
-
- <option value="UTHSC_1107_RankInv">
- HQF BXD Striatum ILM6.1 (Nov07) RankInv
- </option>
-
- <option value="SA_M2_0405_MC">
- HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean
- </option>
-
- <option value="SA_M2_0405_RC">
- HBP Rosen Striatum M430V2 (Apr05) RMA Clean
- </option>
-
- <option value="SA_M2_0405_PC">
- HBP Rosen Striatum M430V2 (Apr05) PDNN Clean
- </option>
-
- <option value="SA_M2_0405_SS">
- HBP Rosen Striatum M430V2 (Apr05) SScore
- </option>
-
- <option value="SA_M2_0405_RR">
- HBP Rosen Striatum M430V2 (Apr05) RMA Orig
- </option>
-
- <option value="Striatum_Exon_0209">
- HQF Striatum Exon (Feb09) RMA
- </option>
-
- <option value="DevStriatum_ILM6.2P14RInv_1110">
- BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **
- </option>
-
- <option value="DevStriatum_ILM6.2P3RInv_1110">
- BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **
- </option>
- </optgroup>
-
- <optgroup label="T Cell (helper) ------">
- <option value="RTHC_0211_R">
- HZI Thelp M430v2 (Feb11) RMA
- </option>
- </optgroup>
-
- <optgroup label="T Cell (regulatory) ------">
- <option value="RTC_1106_R">
- HZI Treg M430v2 (Feb11) RMA
- </option>
- </optgroup>
-
- <optgroup label="Thymus ------">
- <option value="Illum_BXD_Thy_1108">
- UWA Illumina Thymus (Nov08) RSN **
- </option>
- </optgroup>
-
- <optgroup label="Ventral Tegmental Area ------">
- <option value="VCUEtOH_0609_R">
- VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **
- </option>
-
- <option value="VCUSal_0609_R">
- VCU BXD VTA Sal M430 2.0 (Jun09) RMA **
- </option>
-
- <option value="VCUEtvsSal_0609_R">
- VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **
- </option>
- </optgroup>
- </select></td>
- </tr>
-
- <tr>
- <td><span class="ffl fwb fs12">Return:</span></td>
-
- <td><select name="criteria1" size="1">
- <option value="100">
- top 100
- </option>
-
- <option value="200">
- top 200
- </option>
-
- <option value="500" selected>
- top 500
- </option>
-
- <option value="1000">
- top 1000
- </option>
-
- <option value="2000">
- top 2000
- </option>
-
- <option value="5000">
- top 5000
- </option>
-
- <option value="10000">
- top 10000
- </option>
-
- <option value="15000">
- top 15000
- </option>
-
- <option value="20000">
- top 20000
- </option>
- </select></td>
- </tr>
-
- <tr class="mdp1">
- <td><span class="ffl fwb fs12">Samples:</span></td>
-
- <td><select name="MDPChoice1" size="1">
- <option value="1">
- BXD Only
- </option>
-
- <option value="2">
- Non-BXD Only
- </option>
-
- <option value="0">
- All Cases
- </option>
- </select></td>
+ <td><span class="ff1 fwb fs12">Method:</span></td>
+ <td colspan="3">
+ <select name="corr_method" size="1">
+ <option value="sample">Sample r</option>
+ <option value="lit">Literature r</option>
+ <option value="tissue">Tissue r</option>
+ </select>
+ </td>
</tr>
- </table><br>
- Pearson <input type="radio" name="sample_method" value="1" checked>&nbsp;&nbsp;&nbsp;Spearman Rank <input type="radio" name=
- "sample_method" value="2"><br>
- <br>
- <input type="button" name="sample_corr" class="button sample_corr" value=" Compute "><br>
- <br>
- <span class="fs12">The <a href="/correlationAnnotation.html#sample_r" target="_blank">Sample Correlation</a> is computed
- between trait data and any<br>
- other traits in the sample database selected above. Use <a href="/glossary.html#Correlations" target="_blank">Spearman
- Rank</a><br>
- when the sample size is small (&lt;20) or when there are influential outliers.<br></span>
- </td>
- </tr>
- </table>
- </div>
-
- <div id="corrtabs-2">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- <input type="hidden" name="orderBy" value="2">
-
- <table cellpadding="2" cellspacing="0" width="619px">
<tr>
- <td><span class="ffl fwb fs12">Database:</span></td>
-
- <td colspan="3"><select name="database2" size="1">
- <option value="BXDPublish">
- BXD Published Phenotypes
- </option>
-
- <option value="BXDGeno">
- BXD Genotypes
- </option>
-
- <optgroup label="Amygdala ------">
- <option value="INIA_AmgCoh_0311">
- INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA
- </option>
-
- <option value="INIA_Amg_BLA_RMA_1110">
- INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA
- </option>
-
- <option value="INIA_Amg_BLA_RMA_M_1110">
- INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Male
- </option>
-
- <option value="INIA_Amg_BLA_RMA_F_1110">
- INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female
- </option>
- </optgroup>
-
- <optgroup label="Brain ------">
- <option value="BR_M2_1106_R">
- UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA
- </option>
-
- <option value="IBR_M_0606_R">
- INIA Brain mRNA M430 (Jun06) RMA
- </option>
-
- <option value="IBR_M_0106_P">
- INIA Brain mRNA M430 (Jan06) PDNN
- </option>
-
- <option value="IBR_M_0106_R">
- INIA Brain mRNA M430 (Jan06) RMA
- </option>
-
- <option value="BR_U_1105_P">
- UTHSC Brain mRNA U74Av2 (Nov05) PDNN
- </option>
-
- <option value="BR_U_0805_R">
- UTHSC Brain mRNA U74Av2 (Aug05) RMA
- </option>
-
- <option value="BR_U_0805_P">
- UTHSC Brain mRNA U74Av2 (Aug05) PDNN
- </option>
-
- <option value="BR_U_0805_M">
- UTHSC Brain mRNA U74Av2 (Aug05) MAS5
- </option>
-
- <option value="CB_M_0204_P">
- INIA Brain mRNA M430 (Feb04) PDNN
- </option>
- </optgroup>
-
- <optgroup label="Cartilage ------">
- <option value="UCLA_BXDBXH_CARTILAGE_V2">
- UCLA BXD and BXH Cartilage v2
- </option>
-
- <option value="UCLA_BXDBXH_CARTILAGE">
- UCLA BXD and BXH Cartilage
- </option>
-
- <option value="UCLA_BXD_CARTILAGE">
- UCLA BXD Cartilage
- </option>
- </optgroup>
-
- <optgroup label="Cerebellum ------">
- <option value="GCB_M2_0505_M">
- GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5
- </option>
-
- <option value="GCB_M2_0505_P">
- GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN
- </option>
-
- <option value="GCB_M2_0505_R">
- GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA
- </option>
-
- <option value="CB_M_0305_M">
- SJUT Cerebellum mRNA M430 (Mar05) MAS5
- </option>
-
- <option value="CB_M_0305_P">
- SJUT Cerebellum mRNA M430 (Mar05) PDNN
- </option>
-
- <option value="CB_M_0305_R">
- SJUT Cerebellum mRNA M430 (Mar05) RMA
- </option>
-
- <option value="CB_M_1004_M">
- SJUT Cerebellum mRNA M430 (Oct04) MAS5
- </option>
-
- <option value="CB_M_1004_P">
- SJUT Cerebellum mRNA M430 (Oct04) PDNN
- </option>
-
- <option value="CB_M_1004_R">
- SJUT Cerebellum mRNA M430 (Oct04) RMA
- </option>
-
- <option value="CB_M_1003_M">
- SJUT Cerebellum mRNA M430 (Oct03) MAS5
- </option>
- </optgroup>
-
- <optgroup label="Eye ------">
- <option value="Eye_M2_0908_R">
- Eye M430v2 (Sep08) RMA
- </option>
-
- <option value="Eye_M2_0908_R_NB">
- Eye M430v2 Mutant Gpnmb (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_R_ND">
- Eye M430v2 WT Gpnmb (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_R_MT">
- Eye M430v2 Mutant Tyrp1 (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_WTWT">
- Eye M430v2 WT WT (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_R_WT">
- Eye M430v2 WT Tyrp1 (Sep08) RMA **
- </option>
-
- <option value="BXD_GLA_0911">
- BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **
- </option>
- </optgroup>
-
- <optgroup label="Hematopoietic Cells ------">
- <option value="UMCG_0907_HemaStem_ori">
- UMCG Stem Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_HemaStem">
- UMCG Stem Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="UMCG_0907_Pro_ori">
- UMCG Progenitor Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_Pro">
- UMCG Progenitor Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="UMCG_0907_Eryth_ori">
- UMCG Erythroid Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_Eryth">
- UMCG Erythroid Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="UMCG_0907_Myeloid_ori">
- UMCG Myeloid Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_Myeloid">
- UMCG Myeloid Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="HC_U_0304_R">
- GNF Stem Cells U74Av2 (Mar04) RMA
- </option>
- </optgroup>
-
- <optgroup label="Hippocampus ------">
- <option value="HC_M2_0606_P" selected>
- Hippocampus Consortium M430v2 (Jun06) PDNN
- </option>
-
- <option value="HC_M2_0606_M">
- Hippocampus Consortium M430v2 (Jun06) MAS5
- </option>
-
- <option value="HC_M2_0606_R">
- Hippocampus Consortium M430v2 (Jun06) RMA
- </option>
-
- <option value="UMUTAffyExon_0209_RMA">
- UMUTAffy Hippocampus Exon (Feb09) RMA
- </option>
-
- <option value="UT_ILM_BXD_hipp_NON_0909">
- UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_NOS_0909">
- UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_NOE_0909">
- UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_RSS_0909">
- UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_RSE_0909">
- UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv
- </option>
- </optgroup>
-
- <optgroup label="Hypothalamus ------">
- <option value="INIA_Hyp_RMA_1110">
- INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)
- </option>
-
- <option value="INIA_Hyp_M_RMA_1110">
- INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Male
- </option>
-
- <option value="INIA_Hyp_F_RMA_1110">
- INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Female
- </option>
- </optgroup>
-
- <optgroup label="Kidney ------">
- <option value="MA_M2F_0706_R">
- Mouse kidney M430v2 Female (Aug06) RMA
- </option>
-
- <option value="MA_M2M_0706_R">
- Mouse kidney M430v2 Male (Aug06) RMA
- </option>
-
- <option value="MA_M2_0806_R">
- Mouse kidney M430v2 Sex Balanced (Aug06) RMA
- </option>
-
- <option value="MA_M2_0806_P">
- Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN
- </option>
-
- <option value="MA_M2_0706_P">
- Mouse Kidney M430v2 (Jul06) PDNN
- </option>
-
- <option value="MA_M2_0706_R">
- Mouse Kidney M430v2 (Jul06) RMA
- </option>
- </optgroup>
-
- <optgroup label="Leucocytes ------">
- <option value="Illum_BXD_PBL_1108">
- UWA Illumina PBL (Nov08) RSN **
- </option>
- </optgroup>
-
- <optgroup label="Liver ------">
- <option value="GSE16780_UCLA_ML0911">
- GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA
- </option>
-
- <option value="LV_G_0106_F">
- UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females
- </option>
-
- <option value="LV_G_0106_M">
- UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males
- </option>
-
- <option value="LV_G_0106_B">
- UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes
- </option>
-
- <option value="GenEx_BXD_liverSal_RMA_F_0211">
- GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **
- </option>
-
- <option value="GenEx_BXD_liverSal_RMA_M_0211">
- GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **
- </option>
-
- <option value="GenEx_BXD_liverSal_RMA_0211">
- GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **
- </option>
-
- <option value="GenEx_BXD_liverEt_RMA_F_0211">
- GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **
- </option>
-
- <option value="GenEx_BXD_liverEt_RMA_M_0211">
- GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **
- </option>
-
- <option value="GenEx_BXD_liverEt_RMA_0211">
- GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **
- </option>
-
- <option value="SUH_Liv_RMA_0611">
- SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **
- </option>
- </optgroup>
-
- <optgroup label="Lung ------">
- <option value="HZI_0408_R">
- HZI Lung M430v2 (Apr08) RMA
- </option>
-
- <option value="HZI_0408_M">
- HZI Lung M430v2 (Apr08) MAS5
- </option>
- </optgroup>
-
- <optgroup label="Midbrain ------">
- <option value="VUBXDMouseMidBrainQ0512">
- VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile **
- </option>
- </optgroup>
-
- <optgroup label="Muscle ------">
- <option value="EPFLMouseMuscleRMA1211">
- EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **
- </option>
-
- <option value="EPFLMouseMuscleHFDRMA1211">
- EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **
- </option>
-
- <option value="EPFLMouseMuscleCDRMA1211">
- EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **
- </option>
- </optgroup>
-
- <optgroup label="Neocortex ------">
- <option value="DevNeocortex_ILM6.2P14RInv_1111">
- BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv
- </option>
-
- <option value="DevNeocortex_ILM6.2P3RInv_1111">
- BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv
- </option>
-
- <option value="HQFNeoc_1210v2_RankInv">
- HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv
- </option>
-
- <option value="HQFNeoc_1210_RankInv">
- HQF BXD Neocortex ILM6v1.1 (Dec10) RankInv
- </option>
-
- <option value="HQFNeoc_0208_RankInv">
- HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv
- </option>
-
- <option value="DevNeocortex_ILM6.2P14RInv_1110">
- BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv
- </option>
-
- <option value="DevNeocortex_ILM6.2P3RInv_1110">
- BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv
- </option>
- </optgroup>
-
- <optgroup label="Nucleus Accumbens ------">
- <option value="VCUSalo_1007_R">
- VCU BXD NA Sal M430 2.0 (Oct07) RMA
- </option>
-
- <option value="VCUEtOH_1007_R">
- VCU BXD NA EtOH M430 2.0 (Oct07) RMA **
- </option>
-
- <option value="VCUSal_1007_R">
- VCU BXD NA Et vs Sal M430 2.0 (Oct07) Sscore **
- </option>
- </optgroup>
-
- <optgroup label="Prefrontal Cortex ------">
- <option value="VCUEtOH_1206_R">
- VCU BXD PFC EtOH M430 2.0 (Dec06) RMA
- </option>
-
- <option value="VCUSal_1206_R">
- VCU BXD PFC Sal M430 2.0 (Dec06) RMA
- </option>
-
- <option value="VCUSal_1006_R">
- VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore
- </option>
-
- <option value="VCU_PF_Air_0111_R">
- VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **
- </option>
-
- <option value="VCU_PF_Et_0111_R">
- VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **
- </option>
-
- <option value="VCU_PF_AvE_0111_Ss">
- VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **
- </option>
- </optgroup>
-
- <optgroup label="Retina ------">
- <option value="G2NEI_ILM_Retina_BXD_RI0410">
- Normal HEI Retina (April 2010) RankInv
- </option>
-
- <option value="Illum_Retina_BXD_RankInv0410">
- Full HEI Retina (April 2010) RankInv
- </option>
-
- <option value="ONCRetILM6_0412">
- ONC HEI Retina (April 2012) RankInv
- </option>
-
- <option value="B6D2ONCILM_0412">
- B6D2 ONC Retina (April 2012) RankInv **
- </option>
-
- <option value="G2HEIONCRetILM6_0911">
- G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **
- </option>
-
- <option value="HEIONCvsCRetILM6_0911">
- HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **
- </option>
- </optgroup>
-
- <optgroup label="Spleen ------">
- <option value="UTHSC_SPL_RMA_1210">
- UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA
- </option>
-
- <option value="UTHSC_SPL_RMA_1010">
- UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA
- </option>
-
- <option value="IoP_SPL_RMA_0509">
- IoP Affy MOE 430v2 Spleen (May09) RMA
- </option>
-
- <option value="Illum_BXD_Spl_1108">
- UWA Illumina Spleen (Nov08) RSN **
- </option>
-
- <option value="UTK_BXDSpl_VST_0110">
- UTK Spleen ILM6.1 (Jan10) VST
- </option>
- </optgroup>
-
- <optgroup label="Striatum ------">
- <option value="DevStriatum_ILM6.2P14RInv_1111">
- BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **
- </option>
-
- <option value="DevStriatum_ILM6.2P3RInv_1111">
- BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **
- </option>
-
- <option value="UTHSC_Striatum_RankInv_1210">
- HQF BXD Striatum ILM6.1 (Dec10v2) RankInv
- </option>
-
- <option value="UTHSC_Str_RankInv_1210">
- HQF BXD Striatum ILM6.1 (Dec10) RankInv
- </option>
-
- <option value="UTHSC_1107_RankInv">
- HQF BXD Striatum ILM6.1 (Nov07) RankInv
- </option>
-
- <option value="SA_M2_0405_MC">
- HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean
- </option>
-
- <option value="SA_M2_0405_RC">
- HBP Rosen Striatum M430V2 (Apr05) RMA Clean
- </option>
-
- <option value="SA_M2_0405_PC">
- HBP Rosen Striatum M430V2 (Apr05) PDNN Clean
- </option>
-
- <option value="SA_M2_0405_SS">
- HBP Rosen Striatum M430V2 (Apr05) SScore
- </option>
-
- <option value="SA_M2_0405_RR">
- HBP Rosen Striatum M430V2 (Apr05) RMA Orig
- </option>
-
- <option value="Striatum_Exon_0209">
- HQF Striatum Exon (Feb09) RMA
- </option>
-
- <option value="DevStriatum_ILM6.2P14RInv_1110">
- BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **
- </option>
-
- <option value="DevStriatum_ILM6.2P3RInv_1110">
- BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **
- </option>
- </optgroup>
-
- <optgroup label="T Cell (helper) ------">
- <option value="RTHC_0211_R">
- HZI Thelp M430v2 (Feb11) RMA
- </option>
- </optgroup>
-
- <optgroup label="T Cell (regulatory) ------">
- <option value="RTC_1106_R">
- HZI Treg M430v2 (Feb11) RMA
- </option>
- </optgroup>
-
- <optgroup label="Thymus ------">
- <option value="Illum_BXD_Thy_1108">
- UWA Illumina Thymus (Nov08) RSN **
- </option>
- </optgroup>
-
- <optgroup label="Ventral Tegmental Area ------">
- <option value="VCUEtOH_0609_R">
- VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **
- </option>
-
- <option value="VCUSal_0609_R">
- VCU BXD VTA Sal M430 2.0 (Jun09) RMA **
- </option>
-
- <option value="VCUEtvsSal_0609_R">
- VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **
- </option>
- </optgroup>
- </select></td>
- </tr>
-
+ <td><span class="ffl fwb fs12">Database:</span></td>
+ <td colspan="3">
+ <select name="corr_dataset" size="1">
+ {% for tissue in corr_tools.dataset_menu %}
+ {% if tissue.tissue %}
+ <optgroup label="{{ tissue.tissue }} ------">
+ {% endif %}
+ {% for dataset in tissue.datasets %}
+ <option value="{{ dataset[1] }}"
+ {% if corr_tools.dataset_menu_selected == dataset[1] %}
+ selected
+ {% endif %}>
+ {{ dataset[0] }}
+ </option>
+ {% endfor %}
+ {% if tissue.tissue %}
+ </optgroup>
+ {% endif %}
+ {% endfor %}
+ </select>
+ </td>
+ </tr>
+
+
<tr>
<td><span class="ffl fwb fs12">Return:</span></td>
-
- <td><select name="criteria2" size="1">
- <option value="100">
- top 100
- </option>
-
- <option value="200">
- top 200
- </option>
-
- <option value="500" selected>
- top 500
- </option>
-
- <option value="1000">
- top 1000
- </option>
-
- <option value="2000">
- top 2000
- </option>
-
- <option value="5000">
- top 5000
- </option>
-
- <option value="10000">
- top 10000
- </option>
-
- <option value="15000">
- top 15000
- </option>
-
- <option value="20000">
- top 20000
- </option>
- </select></td>
- </tr>
-
- <tr class="mdp2">
- <td><span class="ffl fwb fs12">Samples:</span></td>
-
- <td><select name="MDPChoice2" size="1">
- <option value="1">
- BXD Only
- </option>
-
- <option value="2">
- Non-BXD Only
- </option>
-
- <option value="0">
- All Cases
- </option>
- </select></td>
- </tr>
- </table><br>
- <input type="button" name="lit_corr" class="button lit_corr" value=" Compute "><br>
- <br>
- <span class="fs12">The <a href="/correlationAnnotation.html" target="_blank">Literature Correlation</a> (Lit r) between this
- gene and all other genes is computed<br>
- using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html" target="_blank">Semantic Gene Organizer</a> and human, rat, and
- mouse data from PubMed.<br>
- Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
- <br>
- <a href="/glossary.html#Literature" target="_blank">More on using Lit r</a></span>
- </td>
- </tr>
- </table>
- </div>
-
- <div id="corrtabs-3">
- <table cellpadding="0" cellspacing="0" width="100%">
- <tr>
- <td>
- <input type="hidden" name="orderBy" value="2">
-
- <table cellpadding="2" cellspacing="0" width="619px">
- <tr>
- <td><span class="ffl fwb fs12">Database:</span></td>
-
- <td colspan="3"><select name="database3" size="1">
- <option value="BXDPublish">
- BXD Published Phenotypes
- </option>
-
- <option value="BXDGeno">
- BXD Genotypes
- </option>
-
- <optgroup label="Amygdala ------">
- <option value="INIA_AmgCoh_0311">
- INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA
- </option>
-
- <option value="INIA_Amg_BLA_RMA_1110">
- INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA
- </option>
-
- <option value="INIA_Amg_BLA_RMA_M_1110">
- INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Male
- </option>
-
- <option value="INIA_Amg_BLA_RMA_F_1110">
- INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female
- </option>
- </optgroup>
-
- <optgroup label="Brain ------">
- <option value="BR_M2_1106_R">
- UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA
- </option>
-
- <option value="IBR_M_0606_R">
- INIA Brain mRNA M430 (Jun06) RMA
- </option>
-
- <option value="IBR_M_0106_P">
- INIA Brain mRNA M430 (Jan06) PDNN
- </option>
-
- <option value="IBR_M_0106_R">
- INIA Brain mRNA M430 (Jan06) RMA
- </option>
-
- <option value="BR_U_1105_P">
- UTHSC Brain mRNA U74Av2 (Nov05) PDNN
- </option>
-
- <option value="BR_U_0805_R">
- UTHSC Brain mRNA U74Av2 (Aug05) RMA
- </option>
-
- <option value="BR_U_0805_P">
- UTHSC Brain mRNA U74Av2 (Aug05) PDNN
- </option>
-
- <option value="BR_U_0805_M">
- UTHSC Brain mRNA U74Av2 (Aug05) MAS5
- </option>
-
- <option value="CB_M_0204_P">
- INIA Brain mRNA M430 (Feb04) PDNN
- </option>
- </optgroup>
-
- <optgroup label="Cartilage ------">
- <option value="UCLA_BXDBXH_CARTILAGE_V2">
- UCLA BXD and BXH Cartilage v2
- </option>
-
- <option value="UCLA_BXDBXH_CARTILAGE">
- UCLA BXD and BXH Cartilage
- </option>
-
- <option value="UCLA_BXD_CARTILAGE">
- UCLA BXD Cartilage
- </option>
- </optgroup>
-
- <optgroup label="Cerebellum ------">
- <option value="GCB_M2_0505_M">
- GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5
- </option>
-
- <option value="GCB_M2_0505_P">
- GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN
- </option>
-
- <option value="GCB_M2_0505_R">
- GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA
- </option>
-
- <option value="CB_M_0305_M">
- SJUT Cerebellum mRNA M430 (Mar05) MAS5
- </option>
-
- <option value="CB_M_0305_P">
- SJUT Cerebellum mRNA M430 (Mar05) PDNN
- </option>
-
- <option value="CB_M_0305_R">
- SJUT Cerebellum mRNA M430 (Mar05) RMA
- </option>
-
- <option value="CB_M_1004_M">
- SJUT Cerebellum mRNA M430 (Oct04) MAS5
- </option>
-
- <option value="CB_M_1004_P">
- SJUT Cerebellum mRNA M430 (Oct04) PDNN
- </option>
-
- <option value="CB_M_1004_R">
- SJUT Cerebellum mRNA M430 (Oct04) RMA
- </option>
-
- <option value="CB_M_1003_M">
- SJUT Cerebellum mRNA M430 (Oct03) MAS5
- </option>
- </optgroup>
-
- <optgroup label="Eye ------">
- <option value="Eye_M2_0908_R">
- Eye M430v2 (Sep08) RMA
- </option>
-
- <option value="Eye_M2_0908_R_NB">
- Eye M430v2 Mutant Gpnmb (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_R_ND">
- Eye M430v2 WT Gpnmb (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_R_MT">
- Eye M430v2 Mutant Tyrp1 (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_WTWT">
- Eye M430v2 WT WT (Sep08) RMA **
- </option>
-
- <option value="Eye_M2_0908_R_WT">
- Eye M430v2 WT Tyrp1 (Sep08) RMA **
- </option>
-
- <option value="BXD_GLA_0911">
- BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **
- </option>
- </optgroup>
-
- <optgroup label="Hematopoietic Cells ------">
- <option value="UMCG_0907_HemaStem_ori">
- UMCG Stem Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_HemaStem">
- UMCG Stem Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="UMCG_0907_Pro_ori">
- UMCG Progenitor Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_Pro">
- UMCG Progenitor Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="UMCG_0907_Eryth_ori">
- UMCG Erythroid Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_Eryth">
- UMCG Erythroid Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="UMCG_0907_Myeloid_ori">
- UMCG Myeloid Cells ILM6v1.1 (Apr09) original
- </option>
-
- <option value="UMCG_0907_Myeloid">
- UMCG Myeloid Cells ILM6v1.1 (Apr09) transformed
- </option>
-
- <option value="HC_U_0304_R">
- GNF Stem Cells U74Av2 (Mar04) RMA
- </option>
- </optgroup>
-
- <optgroup label="Hippocampus ------">
- <option value="HC_M2_0606_P" selected>
- Hippocampus Consortium M430v2 (Jun06) PDNN
- </option>
-
- <option value="HC_M2_0606_M">
- Hippocampus Consortium M430v2 (Jun06) MAS5
- </option>
-
- <option value="HC_M2_0606_R">
- Hippocampus Consortium M430v2 (Jun06) RMA
- </option>
-
- <option value="UMUTAffyExon_0209_RMA">
- UMUTAffy Hippocampus Exon (Feb09) RMA
- </option>
-
- <option value="UT_ILM_BXD_hipp_NON_0909">
- UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_NOS_0909">
- UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_NOE_0909">
- UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_RSS_0909">
- UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv
- </option>
-
- <option value="UT_ILM_BXD_hipp_RSE_0909">
- UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv
- </option>
- </optgroup>
-
- <optgroup label="Hypothalamus ------">
- <option value="INIA_Hyp_RMA_1110">
- INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)
- </option>
-
- <option value="INIA_Hyp_M_RMA_1110">
- INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Male
- </option>
-
- <option value="INIA_Hyp_F_RMA_1110">
- INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Female
- </option>
- </optgroup>
-
- <optgroup label="Kidney ------">
- <option value="MA_M2F_0706_R">
- Mouse kidney M430v2 Female (Aug06) RMA
- </option>
-
- <option value="MA_M2M_0706_R">
- Mouse kidney M430v2 Male (Aug06) RMA
- </option>
-
- <option value="MA_M2_0806_R">
- Mouse kidney M430v2 Sex Balanced (Aug06) RMA
- </option>
-
- <option value="MA_M2_0806_P">
- Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN
- </option>
-
- <option value="MA_M2_0706_P">
- Mouse Kidney M430v2 (Jul06) PDNN
- </option>
-
- <option value="MA_M2_0706_R">
- Mouse Kidney M430v2 (Jul06) RMA
- </option>
- </optgroup>
-
- <optgroup label="Leucocytes ------">
- <option value="Illum_BXD_PBL_1108">
- UWA Illumina PBL (Nov08) RSN **
- </option>
- </optgroup>
-
- <optgroup label="Liver ------">
- <option value="GSE16780_UCLA_ML0911">
- GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA
- </option>
-
- <option value="LV_G_0106_F">
- UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females
- </option>
-
- <option value="LV_G_0106_M">
- UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males
- </option>
-
- <option value="LV_G_0106_B">
- UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes
- </option>
-
- <option value="GenEx_BXD_liverSal_RMA_F_0211">
- GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **
- </option>
-
- <option value="GenEx_BXD_liverSal_RMA_M_0211">
- GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **
- </option>
-
- <option value="GenEx_BXD_liverSal_RMA_0211">
- GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **
- </option>
-
- <option value="GenEx_BXD_liverEt_RMA_F_0211">
- GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **
- </option>
-
- <option value="GenEx_BXD_liverEt_RMA_M_0211">
- GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **
- </option>
-
- <option value="GenEx_BXD_liverEt_RMA_0211">
- GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **
- </option>
-
- <option value="SUH_Liv_RMA_0611">
- SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **
- </option>
- </optgroup>
-
- <optgroup label="Lung ------">
- <option value="HZI_0408_R">
- HZI Lung M430v2 (Apr08) RMA
- </option>
-
- <option value="HZI_0408_M">
- HZI Lung M430v2 (Apr08) MAS5
- </option>
- </optgroup>
-
- <optgroup label="Midbrain ------">
- <option value="VUBXDMouseMidBrainQ0512">
- VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile **
- </option>
- </optgroup>
-
- <optgroup label="Muscle ------">
- <option value="EPFLMouseMuscleRMA1211">
- EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **
- </option>
-
- <option value="EPFLMouseMuscleHFDRMA1211">
- EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **
- </option>
-
- <option value="EPFLMouseMuscleCDRMA1211">
- EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **
- </option>
- </optgroup>
-
- <optgroup label="Neocortex ------">
- <option value="DevNeocortex_ILM6.2P14RInv_1111">
- BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv
- </option>
-
- <option value="DevNeocortex_ILM6.2P3RInv_1111">
- BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv
- </option>
-
- <option value="HQFNeoc_1210v2_RankInv">
- HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv
- </option>
-
- <option value="HQFNeoc_1210_RankInv">
- HQF BXD Neocortex ILM6v1.1 (Dec10) RankInv
- </option>
-
- <option value="HQFNeoc_0208_RankInv">
- HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv
- </option>
-
- <option value="DevNeocortex_ILM6.2P14RInv_1110">
- BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv
- </option>
-
- <option value="DevNeocortex_ILM6.2P3RInv_1110">
- BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv
- </option>
- </optgroup>
-
- <optgroup label="Nucleus Accumbens ------">
- <option value="VCUSalo_1007_R">
- VCU BXD NA Sal M430 2.0 (Oct07) RMA
- </option>
-
- <option value="VCUEtOH_1007_R">
- VCU BXD NA EtOH M430 2.0 (Oct07) RMA **
- </option>
-
- <option value="VCUSal_1007_R">
- VCU BXD NA Et vs Sal M430 2.0 (Oct07) Sscore **
- </option>
- </optgroup>
-
- <optgroup label="Prefrontal Cortex ------">
- <option value="VCUEtOH_1206_R">
- VCU BXD PFC EtOH M430 2.0 (Dec06) RMA
- </option>
-
- <option value="VCUSal_1206_R">
- VCU BXD PFC Sal M430 2.0 (Dec06) RMA
- </option>
-
- <option value="VCUSal_1006_R">
- VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore
- </option>
-
- <option value="VCU_PF_Air_0111_R">
- VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **
- </option>
-
- <option value="VCU_PF_Et_0111_R">
- VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **
- </option>
-
- <option value="VCU_PF_AvE_0111_Ss">
- VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **
- </option>
- </optgroup>
-
- <optgroup label="Retina ------">
- <option value="G2NEI_ILM_Retina_BXD_RI0410">
- Normal HEI Retina (April 2010) RankInv
- </option>
-
- <option value="Illum_Retina_BXD_RankInv0410">
- Full HEI Retina (April 2010) RankInv
- </option>
-
- <option value="ONCRetILM6_0412">
- ONC HEI Retina (April 2012) RankInv
- </option>
-
- <option value="B6D2ONCILM_0412">
- B6D2 ONC Retina (April 2012) RankInv **
- </option>
-
- <option value="G2HEIONCRetILM6_0911">
- G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **
- </option>
-
- <option value="HEIONCvsCRetILM6_0911">
- HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **
- </option>
- </optgroup>
-
- <optgroup label="Spleen ------">
- <option value="UTHSC_SPL_RMA_1210">
- UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA
- </option>
-
- <option value="UTHSC_SPL_RMA_1010">
- UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA
- </option>
-
- <option value="IoP_SPL_RMA_0509">
- IoP Affy MOE 430v2 Spleen (May09) RMA
- </option>
-
- <option value="Illum_BXD_Spl_1108">
- UWA Illumina Spleen (Nov08) RSN **
- </option>
-
- <option value="UTK_BXDSpl_VST_0110">
- UTK Spleen ILM6.1 (Jan10) VST
- </option>
- </optgroup>
-
- <optgroup label="Striatum ------">
- <option value="DevStriatum_ILM6.2P14RInv_1111">
- BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **
- </option>
-
- <option value="DevStriatum_ILM6.2P3RInv_1111">
- BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **
- </option>
-
- <option value="UTHSC_Striatum_RankInv_1210">
- HQF BXD Striatum ILM6.1 (Dec10v2) RankInv
- </option>
-
- <option value="UTHSC_Str_RankInv_1210">
- HQF BXD Striatum ILM6.1 (Dec10) RankInv
- </option>
-
- <option value="UTHSC_1107_RankInv">
- HQF BXD Striatum ILM6.1 (Nov07) RankInv
- </option>
-
- <option value="SA_M2_0405_MC">
- HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean
- </option>
-
- <option value="SA_M2_0405_RC">
- HBP Rosen Striatum M430V2 (Apr05) RMA Clean
- </option>
-
- <option value="SA_M2_0405_PC">
- HBP Rosen Striatum M430V2 (Apr05) PDNN Clean
- </option>
-
- <option value="SA_M2_0405_SS">
- HBP Rosen Striatum M430V2 (Apr05) SScore
- </option>
-
- <option value="SA_M2_0405_RR">
- HBP Rosen Striatum M430V2 (Apr05) RMA Orig
- </option>
-
- <option value="Striatum_Exon_0209">
- HQF Striatum Exon (Feb09) RMA
- </option>
-
- <option value="DevStriatum_ILM6.2P14RInv_1110">
- BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **
- </option>
-
- <option value="DevStriatum_ILM6.2P3RInv_1110">
- BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **
- </option>
- </optgroup>
-
- <optgroup label="T Cell (helper) ------">
- <option value="RTHC_0211_R">
- HZI Thelp M430v2 (Feb11) RMA
- </option>
- </optgroup>
-
- <optgroup label="T Cell (regulatory) ------">
- <option value="RTC_1106_R">
- HZI Treg M430v2 (Feb11) RMA
- </option>
- </optgroup>
-
- <optgroup label="Thymus ------">
- <option value="Illum_BXD_Thy_1108">
- UWA Illumina Thymus (Nov08) RSN **
- </option>
- </optgroup>
-
- <optgroup label="Ventral Tegmental Area ------">
- <option value="VCUEtOH_0609_R">
- VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **
- </option>
-
- <option value="VCUSal_0609_R">
- VCU BXD VTA Sal M430 2.0 (Jun09) RMA **
- </option>
-
- <option value="VCUEtvsSal_0609_R">
- VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **
- </option>
- </optgroup>
+
+ <td><select name="corr_return_results" size="1">
+ {% for return_result in corr_tools.return_results_menu %}
+ <option value="{{ return_result }}"
+ {% if corr_tools.return_results_menu_selected == return_result %}
+ selected
+ {% endif %}>
+ Top {{ return_result }}
+ </option>
+ {% endfor %}
</select></td>
</tr>
- <tr>
- <td><span class="ffl fwb fs12">Return:</span></td>
-
- <td><select name="criteria3" size="1">
- <option value="100">
- top 100
- </option>
-
- <option value="200">
- top 200
- </option>
- <option value="500" selected>
- top 500
- </option>
-
- <option value="1000">
- top 1000
- </option>
-
- <option value="2000">
- top 2000
- </option>
-
- <option value="5000">
- top 5000
- </option>
-
- <option value="10000">
- top 10000
- </option>
-
- <option value="15000">
- top 15000
- </option>
-
- <option value="20000">
- top 20000
- </option>
- </select></td>
- </tr>
-
- <tr class="mdp3">
+ <tr class="mdp1">
<td><span class="ffl fwb fs12">Samples:</span></td>
-
- <td><select name="MDPChoice3" size="1">
- <option value="1">
- BXD Only
- </option>
-
- <option value="2">
- Non-BXD Only
- </option>
-
- <option value="0">
- All Cases
- </option>
- </select></td>
+ <td>
+ <select name="corr_samples_group" size="1">
+ {% for group, pretty_group in sample_groups.items() %}
+ <option value="{{ group }}">
+ {{ pretty_group }}
+ </option>
+ {% endfor %}
+ </select>
+ </td>
</tr>
+
</table><br>
- Pearson <input type="radio" name="tissue_method" value="4" checked>&nbsp;&nbsp;&nbsp;Spearman Rank <input type="radio" name=
- "tissue_method" value="5"><br>
+ Pearson <input type="radio" name="sample_method" value="pearson" checked>&nbsp;&nbsp;&nbsp;Spearman Rank <input type="radio" name=
+ "sample_method" value="spearman"><br>
<br>
- <input type="button" name="tiss_corr" class="button tiss_corr" value=" Compute "><br>
+ <input type="button" name="sample_corr" class="button sample_corr" value=" Compute "><br><br>
+ <span id="sample_r_desc" class="correlation_desc fs12">
+ The <a href="/correlationAnnotation.html#sample_r" target="_blank">Sample Correlation</a>
+ is computed
+ between trait data and any<br>
+ other traits in the sample database selected above. Use
+ <a href="/glossary.html#Correlations" target="_blank">Spearman
+ Rank</a><br>
+ when the sample size is small (&lt;20) or when there are influential outliers.
+ </span>
+ <SPAN id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
+ The <A HREF="/correlationAnnotation.html" TARGET="_blank">Literature Correlation</A>
+ (Lit r) between
+ this gene and all other genes is computed<BR>
+ using the <A HREF="https://grits.eecs.utk.edu/sgo/sgo.html" TARGET="_blank">
+ Semantic Gene Organizer</A>
+ and human, rat, and mouse data from PubMed. <BR>
+ Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<BR><BR>
+ <A HREF="/glossary.html#Literature" TARGET="_blank">More on using Lit r</A>
+ </SPAN>
+ <SPAN id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
+ The <A HREF="/webqtl/main.py?FormID=tissueCorrelation" TARGET="_blank">Tissue Correlation</A>
+ (Tissue r)
+ estimates the similarity of expression of two genes<BR>
+ or transcripts across different cells, tissues, or organs
+ (<A HREF="/correlationAnnotation.html#tissue_r" TARGET="_blank">glossary</A>).
+ Tissue correlations<BR>
+ are generated by analyzing expression in multiple samples usually taken from single cases.<BR>
+ <STRONG>Pearson</STRONG> and <STRONG>Spearman Rank</STRONG> correlations have been
+ computed for all pairs of genes<BR> using data from mouse samples.<BR>
+ </SPAN>
<br>
- <span class="fs12">The <a href="/webqtl/main.py?FormID=tissueCorrelation" target="_blank">Tissue Correlation</a> (Tissue r)
- estimates the similarity of expression of two genes<br>
- or transcripts across different cells, tissues, or organs (<a href="/correlationAnnotation.html#tissue_r" target=
- "_blank">glossary</a>). Tissue correlations<br>
- are generated by analyzing expression in multiple samples usually taken from single cases.<br>
- <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been computed for all pairs of genes<br>
- using data from mouse samples.<br></span>
</td>
</tr>
</table>