From 15d64a94eacf6b883fcc1ef2a49aa6ca7934eb96 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 14 May 2019 12:40:18 -0500 Subject: Added all of the third party links from GN1 Fixed issue with the script that generates the drop-down menus where phenotype/genotype datasets wouldn't show up for species without any mRNA assay datasets Added icon for smartphones/tablets Made error more informative for main search Added gene symbol column to collections (need to add something that removes the column if it's all empty) --- wqflask/base/webqtlConfig.py | 15 + wqflask/maintenance/gen_select_dataset.py | 5 +- .../marker_regression/display_mapping_results.py | 2 - wqflask/wqflask/search_results.py | 4 - wqflask/wqflask/show_trait/show_trait.py | 60 ++ wqflask/wqflask/static/new/images/ipad_icon3.png | Bin 0 -> 6728 bytes .../new/javascript/dataset_menu_structure.json | 770 +++++++++++++++++---- wqflask/wqflask/templates/base.html | 2 + wqflask/wqflask/templates/collections/view.html | 7 +- wqflask/wqflask/templates/reference.html | 235 ++++--- wqflask/wqflask/templates/search_error.html | 3 +- wqflask/wqflask/templates/show_trait_details.html | 93 ++- 12 files changed, 939 insertions(+), 257 deletions(-) create mode 100644 wqflask/wqflask/static/new/images/ipad_icon3.png diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index c9052c83..b14cc4b0 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -36,6 +36,21 @@ UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&typ UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' GENOMEBROWSER_URL="https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s" NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=%s" +GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s" +OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s" +UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s" +HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/homologene/?term=%s" +GENOTATION_URL = "http://www.genotation.org/Getd2g.pl?gene_list=%s" +GTEX_URL = "https://www.gtexportal.org/home/gene/%s" +GENEBRIDGE_URL = "https://www.systems-genetics.org/modules_by_gene/%s?organism=%s" +UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgTracks?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s" +BIOGPS_URL = "http://biogps.org/?org=%s#goto=genereport&id=%s" +STRING_URL = "http://string-db.org/newstring_cgi/show_network_section.pl?identifier=%s" +PANTHER_URL = "http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=%s" +GEMMA_URL = "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" +ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=%s" +EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s" +WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s" ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s" DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s' diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index c590a185..be028bdd 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -124,8 +124,9 @@ def get_types(groups): if len(types_list) > 0: types[species][group_name] += types_list else: - types[species].pop(group_name, None) - groups[species] = tuple(group for group in groups[species] if group[0] != group_name) + if not phenotypes_exist(group_name) and not genotypes_exist(group_name): + types[species].pop(group_name, None) + groups[species] = tuple(group for group in groups[species] if group[0] != group_name) else: #ZS: This whole else statement might be unnecessary, need to check types_list = build_types(species, group_name) if len(types_list) > 0: diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 67cefaa6..993fc2d9 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -306,8 +306,6 @@ class DisplayMappingResults(object): for i, indChr in enumerate(self.genotype): self.ChrList.append((indChr.name, i)) - - self.ChrLengthMbList = g.db.execute(""" Select Length from Chr_Length, InbredSet diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 2c8e07dd..12a69bc3 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -175,7 +175,6 @@ views.py). else: combined_where_clause += "OR" else: - logger.debug("Search failed 1") self.search_term_exists = False if self.search_term_exists: combined_where_clause = "(" + combined_where_clause + ")" @@ -184,9 +183,7 @@ views.py). results = the_search.execute(final_query) self.results.extend(results) else: - logger.debug("len(search_terms)<=1") if self.search_terms == []: - logger.debug("Search failed 2") self.search_term_exists = False else: for a_search in self.search_terms: @@ -194,7 +191,6 @@ views.py). if the_search != None: self.results.extend(the_search.run()) else: - logger.debug("Search failed 3") self.search_term_exists = False if self.search_term_exists: diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 53aa1676..cf27a3d7 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -122,6 +122,8 @@ class ShowTrait(object): self.UCSC_BLAT_URL = "" self.UTHSC_BLAT_URL = "" + self.get_external_links() + self.build_correlation_tools() #Get nearest marker for composite mapping @@ -235,6 +237,64 @@ class ShowTrait(object): temp_uuid = self.temp_uuid) self.js_data = js_data + def get_external_links(self): + #ZS: There's some weirdness here because some fields don't exist while others are empty strings + self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.this_trait.pubmed_id if hasattr(self.this_trait, 'pubmed_id') else None + self.ncbi_gene_link = webqtlConfig.NCBI_LOCUSID % self.this_trait.geneid if hasattr(self.this_trait, 'geneid') else None + self.omim_link = webqtlConfig.OMIM_ID % self.this_trait.omim if hasattr(self.this_trait, 'omim') else None + self.unigene_link = webqtlConfig.UNIGEN_ID % tuple(string.split(self.this_trait.unigeneid, '.')[:2]) if (hasattr(self.this_trait, 'unigeneid') and self.this_trait.unigeneid != "") else None + self.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if hasattr(self.this_trait, 'homologeneid') else None + + self.genbank_link = None + if hasattr(self.this_trait, 'genbankid') and self.this_trait.genbankid != None: + genbank_id = '|'.join(self.this_trait.genbankid.split('|')[0:10]) + if genbank_id[-1] == '|': + genbank_id = genbank_id[0:-1] + self.genbank_link = webqtlConfig.GENBANK_ID % genbank_id + + self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = None + self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = None + if self.this_trait.symbol: + self.genotation_link = webqtlConfig.GENOTATION_URL % self.this_trait.symbol + self.gtex_link = webqtlConfig.GTEX_URL % self.this_trait.symbol + self.string_link = webqtlConfig.STRING_URL % self.this_trait.symbol + self.panther_link = webqtlConfig.PANTHER_URL % self.this_trait.symbol + self.ebi_gwas_link = webqtlConfig.EBIGWAS_URL % self.this_trait.symbol + + if self.dataset.group.species == "mouse" or self.dataset.group.species == "human": + self.genebridge_link = webqtlConfig.GENEBRIDGE_URL % (self.this_trait.symbol, self.dataset.group.species) + + if self.dataset.group.species == "mouse": + self.aba_link = webqtlConfig.ABA_URL % self.this_trait.symbol + + query = """SELECT chromosome, txStart, txEnd + FROM GeneList + WHERE geneSymbol = '{}'""".format(self.this_trait.symbol) + + chr, transcript_start, transcript_end = g.db.execute(query).fetchall()[0] if len(g.db.execute(query).fetchall()) > 0 else None + if chr and transcript_start and transcript_end and self.this_trait.refseq_transcriptid: + transcript_start = int(transcript_start*1000000) + transcript_end = int(transcript_end*1000000) + self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('mm10', self.this_trait.refseq_transcriptid, chr, transcript_start, transcript_end) + + if self.dataset.group.species == "rat": + query = """SELECT kgID, chromosome, txStart, txEnd + FROM GeneLink_rn33 + WHERE geneSymbol = '{}'""".format(self.this_trait.symbol) + + kgId, chr, transcript_start, transcript_end = g.db.execute(query).fetchall()[0] if len(g.db.execute(query).fetchall()) > 0 else None + if chr and transcript_start and transcript_end and kgId: + transcript_start = int(transcript_start*1000000) # Convert to bases from megabases + transcript_end = int(transcript_end*1000000) + self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('rn3', kgId, chr, transcript_start, transcript_end) + + if self.this_trait.geneid and (self.dataset.group.species == "mouse" or self.dataset.group.species == "rat" or self.dataset.group.species == "human"): + self.biogps_link = webqtlConfig.BIOGPS_URL % (self.dataset.group.species, self.this_trait.geneid) + self.gemma_link = webqtlConfig.GEMMA_URL % self.this_trait.geneid + + if self.dataset.group.species == "human": + self.aba_link = webqtlConfig.ABA_URL % self.this_trait.geneid + def build_correlation_tools(self): if self.temp_trait == True: this_group = self.temp_group diff --git a/wqflask/wqflask/static/new/images/ipad_icon3.png b/wqflask/wqflask/static/new/images/ipad_icon3.png new file mode 100644 index 00000000..97060e97 Binary files /dev/null and b/wqflask/wqflask/static/new/images/ipad_icon3.png differ diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index ad9e80ab..b2354f70 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -10,7 +10,56 @@ ] } }, - "arabidopsis": {}, + "arabidopsis": { + "BayXSha": { + "Genotypes": [ + [ + "None", + "BayXShaGeno", + "BayXSha Genotypes" + ] + ], + "Phenotypes": [ + [ + "642", + "BayXShaPublish", + "BayXSha Published Phenotypes" + ] + ] + }, + "ColXBur": { + "Genotypes": [ + [ + "None", + "ColXBurGeno", + "ColXBur Genotypes" + ] + ], + "Phenotypes": [ + [ + "623", + "ColXBurPublish", + "ColXBur Published Phenotypes" + ] + ] + }, + "ColXCvi": { + "Genotypes": [ + [ + "None", + "ColXCviGeno", + "ColXCvi Genotypes" + ] + ], + "Phenotypes": [ + [ + "640", + "ColXCviPublish", + "ColXCvi Published Phenotypes" + ] + ] + } + }, "barley": { "QSM": { "Leaf mRNA": [ @@ -67,15 +116,15 @@ "B30_K_1206_M", "Barley1 Leaf MAS 5.0 SCRI (Dec06)" ], - [ - "125", - "B30_K_1206_R", - "Barley1 Leaf gcRMA SCRI (Dec06)" - ], [ "126", "B30_K_1206_Rn", "Barley1 Leaf gcRMAn SCRI (Dec06)" + ], + [ + "125", + "B30_K_1206_R", + "Barley1 Leaf gcRMA SCRI (Dec06)" ] ], "Phenotypes": [ @@ -189,7 +238,7 @@ [ "None", "Aging-Brain-UCIPublish", - "Aging-Brain-UCI Published Phenotypes" + "Aging-Brain-UCI Phenotypes" ] ], "Postcentral Gyrus mRNA": [ @@ -1281,6 +1330,15 @@ ] ] }, + "HCP": { + "Phenotypes": [ + [ + "None", + "HCPPublish", + "HCP Phenotypes" + ] + ] + }, "HLC": { "Liver mRNA": [ [ @@ -1288,15 +1346,15 @@ "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" + ], + [ + "384", + "HLCF_0311", + "GSE9588 Human Liver Normal (Mar11) Females" ] ], "Phenotypes": [ @@ -1442,6 +1500,15 @@ ] ] }, + "Islets-Gerling": { + "Phenotypes": [ + [ + "None", + "Islets-GerlingPublish", + "Islets-Gerling Phenotypes" + ] + ] + }, "TIGEM-Retina-RNA-Seq": { "Phenotypes": [ [ @@ -1490,6 +1557,42 @@ ] ] }, + "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": [ + [ + "657", + "AIL-LGSM-F39-43-GBSPublish", + "AIL F39-43-GBS Phenotypes" + ] + ] + }, "AKXD": { "Genotypes": [ [ @@ -1504,15 +1607,15 @@ "NCI_Agil_Mam_Tum_RMA_0409", "NCI Mammary LMT miRNA v2 (Apr09) RMA" ], - [ - "36", - "MA_M_0704_M", - "NCI Mammary mRNA M430 (July04) MAS5" - ], [ "37", "MA_M_0704_R", "NCI Mammary mRNA M430 (July04) RMA" + ], + [ + "36", + "MA_M_0704_M", + "NCI Mammary mRNA M430 (July04) MAS5" ] ] }, @@ -1579,15 +1682,15 @@ ] ], "Liver mRNA": [ - [ - "38", - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], [ "39", "LVF2_M_0704_R", "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" + ], + [ + "38", + "LVF2_M_0704_M", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" ] ], "Phenotypes": [ @@ -1598,8 +1701,22 @@ ] ] }, + "B6D2": { + "Phenotypes": [ + [ + "None", + "B6D2Publish", + "B6D2 Phenotypes" + ] + ] + }, "B6D2F2": { "Brain mRNA": [ + [ + "77", + "BRF2_M_0805_R", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" + ], [ "76", "BRF2_M_0805_M", @@ -1610,25 +1727,20 @@ "BRF2_M_0805_P", "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" ], - [ - "77", - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], [ "33", "BRF2_M_0304_P", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" ], - [ - "31", - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], [ "32", "BRF2_M_0304_R", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" + ], + [ + "31", + "BRF2_M_0304_M", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" ] ], "Genotypes": [ @@ -1639,6 +1751,22 @@ ] ] }, + "B6D2F2-PSU": { + "Genotypes": [ + [ + "617", + "B6D2F2-PSUGeno", + "B6D2F2-PSU Genotypes" + ] + ], + "Phenotypes": [ + [ + "None", + "B6D2F2-PSUPublish", + "B6D2F2-PSU Phenotypes" + ] + ] + }, "B6D2RI": { "Hippocampus mRNA": [ [ @@ -1690,6 +1818,11 @@ ] ], "Striatum mRNA": [ + [ + "84", + "SA_M2_0905_R", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" + ], [ "83", "SA_M2_0905_M", @@ -1699,26 +1832,21 @@ "85", "SA_M2_0905_P", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ], - [ - "84", - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" ] ] }, "BHF2": { "Adipose mRNA": [ - [ - "197", - "UCLA_BHF2_ADIPOSE_FEMALE", - "UCLA BHF2 Adipose Female mlratio" - ], [ "196", "UCLA_BHF2_ADIPOSE_MALE", "UCLA BHF2 Adipose Male mlratio" ], + [ + "197", + "UCLA_BHF2_ADIPOSE_FEMALE", + "UCLA BHF2 Adipose Female mlratio" + ], [ "165", "UCLA_BHF2_ADIPOSE_0605", @@ -1726,16 +1854,16 @@ ] ], "Brain mRNA": [ - [ - "199", - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], [ "198", "UCLA_BHF2_BRAIN_MALE", "UCLA BHF2 Brain Male mlratio" ], + [ + "199", + "UCLA_BHF2_BRAIN_FEMALE", + "UCLA BHF2 Brain Female mlratio" + ], [ "166", "UCLA_BHF2_BRAIN_0605", @@ -1750,16 +1878,16 @@ ] ], "Liver mRNA": [ - [ - "201", - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], [ "200", "UCLA_BHF2_LIVER_MALE", "UCLA BHF2 Liver Male mlratio" ], + [ + "201", + "UCLA_BHF2_LIVER_FEMALE", + "UCLA BHF2 Liver Female mlratio" + ], [ "167", "UCLA_BHF2_LIVER_0605", @@ -1978,21 +2106,26 @@ "IBR_M_0606_R", "INIA Brain mRNA M430 (Jun06) RMA" ], - [ - "101", - "IBR_M_0106_P", - "INIA Brain mRNA M430 (Jan06) PDNN" - ], [ "102", "IBR_M_0106_R", "INIA Brain mRNA M430 (Jan06) RMA" ], + [ + "101", + "IBR_M_0106_P", + "INIA Brain mRNA M430 (Jan06) PDNN" + ], [ "95", "BR_U_1105_P", "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], + [ + "80", + "BR_U_0805_M", + "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" + ], [ "82", "BR_U_0805_R", @@ -2003,11 +2136,6 @@ "BR_U_0805_P", "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" ], - [ - "80", - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], [ "42", "CB_M_0204_P", @@ -2104,6 +2232,11 @@ "Eye_M2_0908_R_ND", "Eye M430v2 WT Gpnmb (Sep08) RMA" ], + [ + "279", + "Eye_M2_0908_R_WT", + "Eye M430v2 WT Tyrp1 (Sep08) RMA" + ], [ "278", "Eye_M2_0908_R_MT", @@ -2114,11 +2247,6 @@ "Eye_M2_0908_WTWT", "Eye M430v2 WT WT (Sep08) RMA" ], - [ - "279", - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA" - ], [ "400", "DBA2J-ONH-1212", @@ -2402,16 +2530,16 @@ ] ], "Kidney mRNA": [ - [ - "240", - "MA_M2M_0706_R", - "Mouse kidney M430v2 Male (Aug06) RMA" - ], [ "239", "MA_M2F_0706_R", "Mouse kidney M430v2 Female (Aug06) RMA" ], + [ + "240", + "MA_M2M_0706_R", + "Mouse kidney M430v2 Male (Aug06) RMA" + ], [ "118", "MA_M2_0806_R", @@ -2422,37 +2550,27 @@ "MA_M2_0806_P", "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN" ], - [ - "115", - "MA_M2_0706_R", - "Mouse Kidney M430v2 (Jul06) RMA" - ], [ "116", "MA_M2_0706_P", "Mouse Kidney M430v2 (Jul06) PDNN" + ], + [ + "115", + "MA_M2_0706_R", + "Mouse Kidney M430v2 (Jul06) RMA" ] ], "Liver Metabolome": [ [ - "838", - "UTHSC-ETHZ-EPFL_LivPMetExtBHFD0817", - "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, HFD Cohorts (Mar 2017) log2" + "836", + "UTHSC-ETHZ-EPFL_LivPMetExtAHFD0817", + "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction, HFD Cohorts (Jul 2017) log2" ], [ "835", "UTHSC-ETHZ-EPFL_LivPMetExtACD0817", - "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, Chow Diet Cohorts (Mar 2017) log2" - ], - [ - "837", - "UTHSC-ETHZ-EPFL_LivPMetExtBCD0817", - "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, Chow Diet Cohorts (Mar 2017) log2" - ], - [ - "836", - "UTHSC-ETHZ-EPFL_LivPMetExtAHFD0817", - "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD Cohorts (Mar 2017) log2" + "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction, Chow Diet Cohorts (Jul 2017) log2" ], [ "473", @@ -2563,6 +2681,11 @@ "EPFLMouseLiverHFDRMA0413", "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ], + [ + "432", + "EPFLMouseLiverCDRMA0413", + "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" + ], [ "849", "EPFLMouseLiverCDEx0413", @@ -2573,11 +2696,6 @@ "EPFLMouseLiverHFCEx0413", "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" ], - [ - "432", - "EPFLMouseLiverCDRMA0413", - "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" - ], [ "433", "EPFLMouseLiverBothExRMA0413", @@ -2706,21 +2824,21 @@ ] ], "Neocortex mRNA": [ - [ - "374", - "DevNeocortex_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv" - ], [ "375", "DevNeocortex_ILM6.2P14RInv_1111", "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv" ], [ - "284", - "HQFNeoc_1210v2_RankInv", - "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv" - ], + "374", + "DevNeocortex_ILM6.2P3RInv_1111", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv" + ], + [ + "284", + "HQFNeoc_1210v2_RankInv", + "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv" + ], [ "282", "HQFNeoc_1210_RankInv", @@ -2731,15 +2849,15 @@ "HQFNeoc_0208_RankInv", "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" ], - [ - "275", - "DevNeocortex_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" - ], [ "274", "DevNeocortex_ILM6.2P3RInv_1110", "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" + ], + [ + "275", + "DevNeocortex_ILM6.2P14RInv_1110", + "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" ] ], "Nucleus Accumbens mRNA": [ @@ -2971,6 +3089,11 @@ ] ], "Ventral Tegmental Area mRNA": [ + [ + "229", + "VCUEtOH_0609_R", + "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA" + ], [ "228", "VCUSal_0609_R", @@ -2980,11 +3103,15 @@ "230", "VCUEtvsSal_0609_R", "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" - ], + ] + ] + }, + "BXD-Bone": { + "Phenotypes": [ [ - "229", - "VCUEtOH_0609_R", - "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA" + "650", + "BXD-BonePublish", + "BXD-Bone Phenotypes" ] ] }, @@ -3007,7 +3134,7 @@ [ "None", "BXD-HarvestedPublish", - "BXD-NIA-Longevity Phenotypes" + "BXD-Harvested Phenotypes" ] ] }, @@ -3091,6 +3218,22 @@ ] ] }, + "C57BL-6JxC57BL-6NJF2": { + "Genotypes": [ + [ + "622", + "C57BL-6JxC57BL-6NJF2Geno", + "C57BL-6JxC57BL-6NJF2 Genotypes" + ] + ], + "Phenotypes": [ + [ + "620", + "C57BL-6JxC57BL-6NJF2Publish", + "C57BL/6JxC57BL/6NJ F2 CROSS Phenotypes" + ] + ] + }, "CFW": { "Hippocampus mRNA": [ [ @@ -3190,6 +3333,15 @@ ] ] }, + "CMS": { + "Phenotypes": [ + [ + "None", + "CMSPublish", + "CMS Phenotypes" + ] + ] + }, "CTB6F2": { "Adipose mRNA": [ [ @@ -3290,15 +3442,15 @@ ] ], "Hippocampus mRNA": [ - [ - "99", - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], [ "100", "HC_M2CB_1205_R", "Hippocampus Consortium M430v2 CXB (Dec05) RMA" + ], + [ + "99", + "HC_M2CB_1205_P", + "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" ] ], "Liver mRNA": [ @@ -3387,6 +3539,16 @@ ] ], "Hippocampus mRNA": [ + [ + "213", + "Illum_LXS_Hipp_NOS_1008", + "Hippocampus Illumina NOS (Oct08) RankInv beta" + ], + [ + "219", + "Illum_LXS_Hipp_NON_1008", + "Hippocampus Illumina NON (Oct08) RankInv beta" + ], [ "212", "Illum_LXS_Hipp_RSE_1008", @@ -3402,16 +3564,6 @@ "Illum_LXS_Hipp_RSS_1008", "Hippocampus Illumina RSS (Oct08) RankInv beta" ], - [ - "213", - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], - [ - "219", - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" - ], [ "143", "Illum_LXS_Hipp_loess0807", @@ -3463,6 +3615,22 @@ ] ] }, + "Linsenbardt-Boehm": { + "Genotypes": [ + [ + "None", + "Linsenbardt-BoehmGeno", + "Linsenbardt-Boehm Genotypes" + ] + ], + "Phenotypes": [ + [ + "645", + "Linsenbardt-BoehmPublish", + "Linsenbardt-Boehm Published Phenotypes" + ] + ] + }, "MDP": { "Bone Femur mRNA": [ [ @@ -3486,15 +3654,15 @@ ] ], "Hippocampus mRNA": [ - [ - "272", - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], [ "273", "UMUTAffyExon_0209_RMA_MDP", "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" + ], + [ + "272", + "HC_M2_0606_MDP", + "Hippocampus Consortium M430v2 (Jun06) RMA MDP" ] ], "Liver mRNA": [ @@ -3580,9 +3748,28 @@ "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Siamak" ] ] + }, + "SOTNOT-OHSU": { + "Genotypes": [ + [ + "613", + "SOTNOT-OHSUGeno", + "SOTNOT-OHSU Genotypes" + ] + ] + } + }, + "poplar": { + "Poplar": { + "Phenotypes": [ + [ + "649", + "PoplarPublish", + "Poplar Phenotypes" + ] + ] } }, - "poplar": {}, "rat": { "HSNIH-Palmer": { "Infralimbic Cortex mRNA": [ @@ -3628,6 +3815,15 @@ ] ] }, + "HSNIH-RGSMC": { + "Phenotypes": [ + [ + "None", + "HSNIH-RGSMCPublish", + "HSNIH-RGSMC Phenotypes" + ] + ] + }, "HXBBXH": { "Adipose mRNA": [ [ @@ -3718,8 +3914,44 @@ ] } }, - "soybean": {}, - "tomato": {} + "soybean": { + "J12XJ58F11": { + "Genotypes": [ + [ + "None", + "J12XJ58F11Geno", + "J12XJ58F11 Genotypes" + ] + ], + "Phenotypes": [ + [ + "647", + "J12XJ58F11Publish", + "J12XJ58F11 Phenotypes" + ] + ] + }, + "J12XJ58F2": { + "Phenotypes": [ + [ + "616", + "J12XJ58F2Publish", + "J12XJ58F2 Published Phenotypes" + ] + ] + } + }, + "tomato": { + "LXP": { + "Phenotypes": [ + [ + "621", + "LXPPublish", + "LXP Published Phenotypes" + ] + ] + } + } }, "groups": { "All Species": [ @@ -3728,7 +3960,20 @@ "All Groups" ] ], - "arabidopsis": [], + "arabidopsis": [ + [ + "BayXSha", + "BayXSha" + ], + [ + "ColXBur", + "ColXBur" + ], + [ + "ColXCvi", + "ColXCvi" + ] + ], "barley": [ [ "QSM", @@ -3766,6 +4011,10 @@ "Aging-Brain-UCI", "Brain, Aging: Normal Gene Expression (UCI/Cotman)" ], + [ + "HCP", + "Brain, Cognition, Human Connectome Project" + ], [ "HSB", "Brain, Development: Normal Gene Expression (Yale/Sestan)" @@ -3798,6 +4047,10 @@ "CEPH-2004", "Lymphoblastoid Cells: Gene Expression (CEPH, Williams)" ], + [ + "Islets-Gerling", + "Pancreatic: Islets (UTHSC/Gerling)" + ], [ "TIGEM-Retina-RNA-Seq", "Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)" @@ -3808,6 +4061,22 @@ "AIL", "AIL Advanced Intercross Line" ], + [ + "AIL-LGSM-F34-A", + "AIL LGSM F34 (Array)" + ], + [ + "AIL-LGSM-F34-GBS", + "AIL LGSM F34 (GBS)" + ], + [ + "AIL-LGSM-F34-F39-43-GBS", + "AIL LGSM F34 and F39-43 (GBS)" + ], + [ + "AIL-LGSM-F39-43-GBS", + "AIL LGSM F39-43 (GBS)" + ], [ "AKXD", "AKXD RI Family" @@ -3820,10 +4089,18 @@ "B6BTBRF2", "B6BTBRF2" ], + [ + "Linsenbardt-Boehm", + "B6D2 EtOH Selected Advanced Intercross" + ], [ "B6D2F2", "B6D2F2" ], + [ + "B6D2F2-PSU", + "B6D2F2 PSU" + ], [ "BDF2-1999", "BDF2 UCLA" @@ -3844,6 +4121,10 @@ "B6D2RI", "BXD Aged" ], + [ + "BXD-Bone", + "BXD Bone Individual Data" + ], [ "BXD-Harvested", "BXD NIA Longevity Study" @@ -3876,6 +4157,10 @@ "CIE-RMA", "Chronic Intermittent Ethanol Phase 2" ], + [ + "CMS", + "Chronic Mild Stress" + ], [ "CXB", "CXB RI Family (strain means)" @@ -3884,6 +4169,10 @@ "D2GM", "D2 Glaucoma Model" ], + [ + "B6D2", + "Glaucoma and Aged Retina, UTHSC" + ], [ "HS", "Heterogeneous Stock" @@ -3904,12 +4193,25 @@ "NZBXFVB-N2", "NZB/FVB N2 NCI" ], + [ + "C57BL-6JxC57BL-6NJF2", + "Reduced Complexity Cross (B6JxB6N F2)" + ], [ "Retina-RGC-Rheaume", "Retina RGC Rheaume" + ], + [ + "SOTNOT-OHSU", + "SOTNOT-OHSU" + ] + ], + "poplar": [ + [ + "Poplar", + "Poplar" ] ], - "poplar": [], "rat": [ [ "HXBBXH", @@ -3919,13 +4221,31 @@ "HSNIH-Palmer", "NIH Heterogeneous Stock (Palmer)" ], + [ + "HSNIH-RGSMC", + "NIH Heterogeneous Stock (RGSMC 2013)" + ], [ "SRxSHRSPF2", "UIOWA SRxSHRSP F2" ] ], - "soybean": [], - "tomato": [] + "soybean": [ + [ + "J12XJ58F11", + "J12XJ58F11" + ], + [ + "J12XJ58F2", + "J12XJ58F2" + ] + ], + "tomato": [ + [ + "LXP", + "LXP" + ] + ] }, "species": [ [ @@ -3978,7 +4298,38 @@ ] ] }, - "arabidopsis": {}, + "arabidopsis": { + "BayXSha": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], + "ColXBur": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], + "ColXCvi": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ] + }, "barley": { "QSM": [ [ @@ -4518,6 +4869,12 @@ "Primary Visual Cortex mRNA" ] ], + "HCP": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "HLC": [ [ "Phenotypes", @@ -4604,6 +4961,12 @@ "Ventrolateral Prefrontal Cortex mRNA" ] ], + "Islets-Gerling": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "TIGEM-Retina-RNA-Seq": [ [ "Phenotypes", @@ -4634,6 +4997,30 @@ "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" + ] + ], "AKXD": [ [ "Genotypes", @@ -4684,6 +5071,12 @@ "Liver mRNA" ] ], + "B6D2": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "B6D2F2": [ [ "Genotypes", @@ -4694,6 +5087,16 @@ "Brain mRNA" ] ], + "B6D2F2-PSU": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], "B6D2RI": [ [ "Phenotypes", @@ -4910,6 +5313,12 @@ "Ventral Tegmental Area mRNA" ] ], + "BXD-Bone": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "BXD-Harvested": [ [ "Phenotypes", @@ -4960,6 +5369,16 @@ "Liver mRNA" ] ], + "C57BL-6JxC57BL-6NJF2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], "CFW": [ [ "Phenotypes", @@ -5002,6 +5421,12 @@ "Midbrain mRNA" ] ], + "CMS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "CTB6F2": [ [ "Phenotypes", @@ -5106,6 +5531,16 @@ "Prefrontal Cortex mRNA" ] ], + "Linsenbardt-Boehm": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], "MDP": [ [ "Phenotypes", @@ -5155,9 +5590,22 @@ "Retina Single-cell RNA-Seq", "Retina Single-cell RNA-Seq" ] + ], + "SOTNOT-OHSU": [ + [ + "Genotypes", + "Genotypes" + ] + ] + }, + "poplar": { + "Poplar": [ + [ + "Phenotypes", + "Phenotypes" + ] ] }, - "poplar": {}, "rat": { "HSNIH-Palmer": [ [ @@ -5185,6 +5633,12 @@ "Prelimbic Cortex mRNA" ] ], + "HSNIH-RGSMC": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "HXBBXH": [ [ "Phenotypes", @@ -5230,7 +5684,31 @@ ] ] }, - "soybean": {}, - "tomato": {} + "soybean": { + "J12XJ58F11": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], + "J12XJ58F2": [ + [ + "Phenotypes", + "Phenotypes" + ] + ] + }, + "tomato": { + "LXP": [ + [ + "Phenotypes", + "Phenotypes" + ] + ] + } } } \ No newline at end of file diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 3d03f3b9..2c1f67d4 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -7,6 +7,8 @@ {% block title %}{% endblock %} GeneNetwork + + diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index c9c44796..8d22b2a8 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -102,6 +102,7 @@ Index Dataset Record + Symbol Description Location Mean @@ -128,13 +129,17 @@ {{ this_trait.name }} + {% if this_trait.symbol %} + {{ this_trait.symbol }} + {% else %} + N/A + {% endif %} {{ this_trait.description_display }} {{ this_trait.location_repr }} {{ '%0.3f' % this_trait.mean|float }} {{ '%0.3f' % this_trait.LRS_score_repr|float }} {{ this_trait.LRS_location_repr }} {{ '%0.3f' % this_trait.additive|float }} - {% endfor %} diff --git a/wqflask/wqflask/templates/reference.html b/wqflask/wqflask/templates/reference.html index c559d68f..d95d22e3 100644 --- a/wqflask/wqflask/templates/reference.html +++ b/wqflask/wqflask/templates/reference.html @@ -2,7 +2,7 @@ {% block title %}References{% endblock %} {% block content %} -

Papers and References to GeneNetwork

+

 Papers and References to GeneNetwork

@@ -14,6 +14,9 @@

+2020 | +2019 | +2018 | 2017 | 2016 | 2015 | @@ -30,35 +33,44 @@ 2004 | 2003 | -
+ + Google Scholar search for "genenetwork" OR "webqtl" generated: +
    +
  1. 1430 hits on 2016/09/08 +
  2. 1730 hits on 2017/10/17 +
  3. 2020 hits on 2019/05/13) +
+Google Scholar search for "genenetwork.org" generated: -
- Highlighted References -
+
    +
  1. 1030 hits on 2019/05/13 +
  2. 105 hits from 2018/01/01 to 2019/05/13 +
-Please send us citations to articles that we may have missed. +
 -
-
- Google Scholar search for "genenetwork" OR "webqtl" (1430 hits as of September 8, 2016, 1730 as of Oct 18, 2017). - +
+ Highlighted References +
+ +Please send us citations to articles that we may have missed.
  1. Mulligan MK, Mozhui K, Prins P, Williams RW (2017) GeneNetwork: A Toolbox for Systems Genetics. In Systems Genetics, Methods in Molecular Biology 1488:75-120 [An updated primer in using GeneNetwork for molecular analysis of mouse and human cohorts.] -PDF version +PDF version

    -
  2. Williams RW, Williams EG (2017) Resources for Systems Genetics. In Systems Genetics, Methods in Molecular Biology 1488:3-29. +
  3. Williams RW, Williams EG (2017) Resources for Systems Genetics. In Systems Genetics, Methods in Molecular Biology 1488:3-29. [This review is intended to help you when making the hard choices about types of resources to use in system genetic studies. The short answer: embrace diversity in your resources. The computational barriers to joint analysis are now minimal.] -PDF version +PDF version

    @@ -73,7 +85,7 @@
  4. Pinelli M, Carissimo A, Cutillo L, Lai CH, Mutarelli M, Moretti MN, Singh MV, Karali M, Carrella D, Pizzo M, Russo F, Ferrari S, Ponzin D, Angelini C, Banfi S, di Bernardo D (2016) An atlas of gene expression and gene co-regulation in the human retina.Nucleic Acids Res. 2016 Jul 8;44(12):5773-84 -RETINA database, and see the PDF. These data are now in GeneNetwork (Species = Human, Group = Retina). +RETINA database, and see the PDF. These data are now in GeneNetwork (Species = Human, Group = Retina).
    @@ -82,7 +94,7 @@ Pinelli M, Carissimo A, Cutillo L, Lai CH, Mutarelli M, Moretti MN, Singh MV, Ka
  5. Williams EG, Wu Y, Pooja J, Dubuis S, Blattmann P, Argmann CA, Houten SM, Amariuta T, Wolski W, Zamboni N, Aebersold R, Auwerx J (2016) Systems proteomics and trans-omic integration illuminate new mechanisms in mitochondrial function. Science 352(6291):aad0189 -HTML version, PDF +HTML version, PDF

    @@ -97,7 +109,7 @@ Sloan Z, Arends D, Broman KW, Centeno A, Furlotte N, Nijveen H, Yan L, Zhou X, W
  6. Alam G, Miller DB, O'Callaghan JP, Lu L, Williams RW, Jones BC (2016) MPTP neurotoxicity is highly concordant between the sexes among BXD recombinant inbred mouse strains. Neurotoxicology in press -PDF version +PDF version

    @@ -111,9 +123,9 @@ Sloan Z, Arends D, Broman KW, Centeno A, Furlotte N, Nijveen H, Yan L, Zhou X, W
  7. Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW (2016). Joint mouse-human phenome-wide association to test gene function and disease risk. Nature Communications 7:10464 [Best reference on the BXD family of strains and the wide range of phenotypes that have been generated over the past 40 years.] -PDF version and the +PDF version and the -Supplementary Tables in one Excel file +Supplementary Tables in one Excel file
    @@ -160,7 +172,7 @@ Ye R, Carneiro AM, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B,

  8. -Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW, Auwerx J (2013) Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497:451-457 PDF version +Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW, Auwerx J (2013) Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497:451-457 PDF version

    @@ -180,7 +192,7 @@ Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW -
    +
    Key References
    @@ -192,15 +204,15 @@ Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW
  9. Mulligan MK, Mozhui K, Prins P, Williams RW (2016) GeneNetwork – A toolbox for systems genetics. In Systems Genetics, Methods in Molecular Biology; Schughart K, Williams RW eds.; Humana Press, in press [This is a currently the most comprehensive protocol and guide (20 Mb) for GeneNetwork.] -PDF version +PDF version
  10. Williams RW, Mulligan MK (2012) Genetic and molecular network analysis of behavior. Int Rev Neurobiol. 104:135-57. [Explains the use of GeneNetwork in behavioral neurogenetics] -PDF version +PDF version -
  11. Williams EG, Auwerx J (2015) The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. [Research into the genetic and environmental factors behind complex trait variation has traditionally been segregated into distinct scientific camps. The reductionist approach aims to decrypt phenotypic variability bit by bit, founded on the underlying hypothesis that genome-to-phenome relations are largely constructed from the additive effects of their molecular players. In contrast, the systems approach aims to examine large-scale interactions of many components simultaneously, on the premise that interactions in gene networks can be both linear and non-linear. Both approaches are complementary, and they are becoming increasingly intertwined due to developments in gene editing tools, omics technologies, and population resources. Together, these strategies are beginning to drive the next era in complex trait research, paving the way to improve agriculture and toward more personalized medicine.] PDF version +
  12. Williams EG, Auwerx J (2015) The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. [Research into the genetic and environmental factors behind complex trait variation has traditionally been segregated into distinct scientific camps. The reductionist approach aims to decrypt phenotypic variability bit by bit, founded on the underlying hypothesis that genome-to-phenome relations are largely constructed from the additive effects of their molecular players. In contrast, the systems approach aims to examine large-scale interactions of many components simultaneously, on the premise that interactions in gene networks can be both linear and non-linear. Both approaches are complementary, and they are becoming increasingly intertwined due to developments in gene editing tools, omics technologies, and population resources. Together, these strategies are beginning to drive the next era in complex trait research, paving the way to improve agriculture and toward more personalized medicine.] PDF version
  13. @@ -253,7 +265,7 @@ Manly KF, Wang J, Williams RW ( Manly K, Williams RW (2001) WEBQTL—WWW service for mapping quantitative trait loci. International Mouse Genome Conference 15: 74. [First published abstract on WebQTL, presented Oct 2001, Edinburgh; also see 2002 CTC abstract]
  14. -Taylor BA, Heiniger HJ, Meier H (1973) Genetic analysis of resistance to cadmium-induced teticular damage in mice. Proc Soc Exp Biol Med 143:629-33 [This is one of the first full paper on the use of recombinant inbred strains in biomedical research and the first paper to use BXD lines of mice. The cdm locus that they mapped to distal Chr 3 was subsequently defined as the Slc38a8 metal testicular metal ion transporter. Full text +Taylor BA, Heiniger HJ, Meier H (1973) Genetic analysis of resistance to cadmium-induced teticular damage in mice. Proc Soc Exp Biol Med 143:629-33 [This is one of the first full paper on the use of recombinant inbred strains in biomedical research and the first paper to use BXD lines of mice. The cdm locus that they mapped to distal Chr 3 was subsequently defined as the Slc38a8 metal testicular metal ion transporter. Full text
  15. Webster JA, Gibbs JR, Clarke J, Ray M, Zhang W, Holmans P, Rohrer K, Zhao A, Marlowe L, Kaleem M, McCorquodale DS 3rd, Cuello C, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV; NACC-Neuropathology Group, Heward CB, Reiman EM, Stephan D, Hardy J, Myers AJ (2009) Genetic control of human brain transcript expression in Alzheimer disease. Am J Hum Genet 84:445-58. [Please review and cite this article if you have used the HUMAN data set by Myers and colleagues in GeneNetwork.]
  16. @@ -264,20 +276,70 @@ Zhang B, Schmoyer D, Kirov S, Snoddy J ( + GeneNetwork (2019) (not complete) +
    + +
    +
      + +
    1. +Théberge ET, Baker JA, Dubose C, Boyle JK, Balce K, Goldowitz D, Hamre KM (2019) Genetic influences on the amount of cell death in the neural tube of BXD mice exposed to acute ethanol at midgestation. Alcohol Clin Exp Res 43:439-452 +
    2. +Roy S, Zaman KI, Williams RW, Homayouni R (2019) Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion. BMC Bioinformatics 20(Suppl 2):104 + +
    +
    17. -
    - GeneNetwork (2017) +
    + GeneNetwork (2018) (not complete)
      +
    1. Ashbrook DG, Mulligan MK, Williams RW Post-genomic behavioral genetics: From revolution to routine (2018) Genes Brain Behav 17:e12441 +
    2. +de Vries M, Faiz A, Woldhuis RR, Postma DS, de Jong TV, Sin DD, Bossé Y, Nickle DC, Guryev V, Timens W, van den Berge M, Brandsma CA (2018) Lung tissue gene-expression signature for the ageing lung in COPD. Thorax 73:609-617 +
    3. +Diessler S, Jan M, Emmenegger Y, Guex N, Middleton B, Skene DJ, Ibberson M, Burdet F, Götz L, Pagni M, Sankar M, Liechti R, Hor CN, Xenarios I, Franken P (2018) A systems genetics resource and analysis of sleep regulation in the mouse. PLoS Biology 16(8):e2005750 +
    4. +King R, Struebing FL, Li Y, Wang J, Koch AA, Cooke Bailey JN, Gharahkhani P; International Glaucoma Genetics Consortium; NEIGHBORHOOD Consortium, MacGregor S, Allingham RR, Hauser MA, Wiggs JL, Geisert EE (2018) Genomic locus modulating corneal thickness in the mouse identifies POU6F2 as a potential risk of developing glaucoma. PLoS Genet 14:e1007145 +
    5. +Lu Y, Zhou D, King R, Zhu S, Simpson CL, Jones BC, Zhang W, Geisert EE, Lu L (2018) The genetic dissection of Myo7a gene expression in the retinas of BXD mice. Mol Vis 24:115-126 +
    6. +Struebing FL, King R, Li Y, Cooke Bailey JN; NEIGHBORHOOD consortium, Wiggs JL, Geisert EE (2018) Genomic loci modulating retinal ganglion cell death following elevated IOP in the mouse. Exp Eye Res 169:61-67 + + +
    +
    + + + + +
    + GeneNetwork (2017) (not complete) +
    + +
    +
      + +
    1. +Baker JA, Li J, Zhou D, Yang M, Cook MN, Jones BC, Mulligan MK, Hamre KM, Lu L (2017) Analyses of differentially expressed genes after exposure to acute stress, acute ethanol, or a combination of both in mice. Alcohol 58:139-151
    2. Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O (2017) Genetic variation in the social environment contributes to health and disease. PLoS Genet 13(1):e1006498 +
    3. Brockmann GA, Arends D, Heise S, Dogan A (2017) Systems genetics of obesity. Methods Mol Biol. 2017;1488:481-497 +
    4. +Grisham W, Brumberg JC, Gilbert T, Lanyon L, Williams RW, Olivo R (2017) Teaching with Big Data: Report from the 2016 Society for Neuroscience Teaching Workshop. J Undergrad Neurosci Educ 16:A68-A76 +
    5. + +Jones BC, Jellen LC (2017) Systems genetics analysis of iron and its regulation in brain and periphery. Methods Mol Biol 1488:467-480
    6. Lopez MF, Miles MF, Williams RW, Becker HC (2017) Variable effects of chronic intermittent ethanol exposure on ethanol drinking in a genetically diverse mouse cohort. Alcohol 58:73-82
    7. +Parker CC, Dickson PE, Philip VM, Thomas M, Chesler EJ (2017) Curr Protoc Neurosci 79:8.39.1-8.39.20 +
    8. Porcu P, O'Buckley TK, Lopez MF, Becker HC, Miles MF, Williams RW, Morrow AL (2017) Initial genetic dissection of serum neuroactive steroids following chronic intermittent ethanol across BXD mouse strains. Alcohol 58:107-125
    9. Rinker JA, Fulmer DB, Trantham-Davidson H, Smith ML, Williams RW, Lopez MF, Randall PK, Chandler LJ, Miles MF, Becker HC, Mulholland PJ (2017) Differential potassium channel gene regulation in BXD mice reveals novel targets for pharmacogenetic therapies to reduce heavy alcohol drinking. Alcohol 58:33-45 @@ -290,7 +352,7 @@ van der Vaart AD, Wolstenholme JT, Smith ML, Harris GM, Lopez MF, Wolen AR, Beck -
      +
      GeneNetwork (2016)
      @@ -325,7 +387,7 @@ Williams EG, Wu Y, Jha P, Dubuis S, Blattmann P, Argmann CA, Houten SM, Amariuta -
      +
      GeneNetwork (2015)
      @@ -337,7 +399,7 @@ Ashbrook DG, Gini B, Hager R ( Ashbrook DG, Williams RW, Lu L, Hager R (2015) A cross-species genetic analysis identifies candidate genes for mouse anxiety and human bipolar disorder. Frontiers in Behavioral Neuroscience 9:171
    10. -Chaum E, Winborn CS, Bhattacharya S (2015) Genomic regulation of senescence and innate immunity signaling in the retinal pigment epithelium. Mammalian Genome 26:210-221 Full text +Chaum E, Winborn CS, Bhattacharya S (2015) Genomic regulation of senescence and innate immunity signaling in the retinal pigment epithelium. Mammalian Genome 26:210-221 Full text
    11. Cheng Q, Seltzer Z, Sima C, Lakschevitz FS, Glogauer M (2015) Quantitative trait loci and candidate genes for neutrophil recruitment in sterile inflammation mapped in AXB-BXA recombinant inbred mice. PLoS One 10:e0124117
    12. @@ -359,7 +421,7 @@ Shea CJ, Carhuatanta KA, Wagner J, Bechmann N, Moore R, Herman JP, Jankord R (<
    13. Xue Y, Li J, Yan L, Lu L, Liao FF (2015) Genetic variability to diet-induced hippocampal dysfunction in BXD recombinant inbred (RI) mouse strains. Behav Brain Res 292:83-94
    14. -Williams EG, Auwerx J (2015) The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. PDF version +Williams EG, Auwerx J (2015) The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. PDF version
    @@ -374,7 +436,7 @@ Williams EG, Auwerx J ( +
    GeneNetwork (2014)
    @@ -413,7 +475,7 @@ Keeley PW, Zhou C, Lu L, Williams RW, Melmed S, Reese BE (2014) Sirt1 induction confers resistance to etoposide-induced genotoxic apoptosis in thyroid cancers. Int J Oncol 45:2065-2075
  17. -Loos M, Mueller T, Gouwenberg Y, Wijnands R, van der Loo RJ, Birchmeier C, Smit AB, Spijker S (2014) Neuregulin-3 in the mouse medial prefrontal cortex regulates impulsive action. Biol Psychiatry 76:648-655 +Loos M, Mueller T, Gouwenberg Y, Wijnands R, van der Loo RJ, Birchmeier C, Smit AB, Spijker S (2014) Neuregulin-3 in the mouse medial prefrontal cortex regulates impulsive action. Biol Psychiatry 76:648-655
  18. Lotan A, Fenckova M, Fralten J, Alttoa A, Dixson L, Williams RW, van der Voet M (2014) Neuroinformatic analyses of common and distinct genetic components associate with major neuropsychiatric disorders. Frontiers in Neuroscience 8:331
  19. @@ -471,7 +533,7 @@ Ye R, Carneiro AM, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B, -
    +
    GeneNetwork (2013)
    @@ -481,7 +543,7 @@ Ye R, Carneiro AM, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B,
  20. Bhandari P, Hill JS, Farris SP, Costin B, Martin I, Chan CL, Alaimo JT, Bettinger JC, Davies AG, Miles MF, Grotewiel M (2013) Chloride intracellular channels modulate acute ethanol behaviors in Drosophila, Caenorhabditis elegans and mice. Genes, Brain & Behavior 11:387-97
  21. -Cheng Y, Gaughan J, Midic U, Han Z, Liang CG, Patel BG, Latham KE (2013) Systems genetics implicates cytoskeletal genes in oocyte control of cloned embryo quality. Genetics 193:877-896 PDF version +Cheng Y, Gaughan J, Midic U, Han Z, Liang CG, Patel BG, Latham KE (2013) Systems genetics implicates cytoskeletal genes in oocyte control of cloned embryo quality. Genetics 193:877-896 PDF version
  22. Dogan A, Lasch P, Neuschl C, Millrose MK, Alberts R, Schughart K, Naumann D, Brockmann GA. (2013) ATR-FTIR spectroscopy reveals genomic loci regulating the tissue response in high fat diet fed BXD recombinant inbred mouse strains. BMC Genomics 14:386
  23. @@ -489,7 +551,7 @@ DuBose CS, Chesler EJ, Goldowitz D, Hamre KM (2013) Fyn-dependent gene networks in acute ethanol sensitivity. PLoS One 8:e82435
  24. -Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW, Auwerx J (2013) Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497:451-457 PDF version +Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW, Auwerx J (2013) Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497:451-457 PDF version
  25. Huang Y, Wang L, Bennett B, Williams RW, Wang YJ, Gu WK, Jiao Y (2013) Potential role of Atp5g3 in epigenetic regulation of alcohol preference or obesity from a mouse genomic perspective. Genet Mol Res 12:3662-3674
  26. @@ -537,7 +599,7 @@ Vanderlinden LA, Saba LM, Kechris K, Miles MF, Hoffman PL, Tabakoff B ( +
    GeneNetwork (2012)
    @@ -553,7 +615,7 @@ Boughter JD Jr, Mulligan MK, St John SJ, Tokita K, Lu L, Heck DH, Williams RW (<
  27. Bubier JA, Chesler EJ (2012) Accelerating discovery for complex neurological and behavioral disorders through systems genetics and integrative genomics in the laboratory mouse. Neurotherapeutics 9:338-348 Full Text version
  28. -Bryant CD, Kole LA, Guido MA, Sokoloff G, Palmer AA (2012) Congenic dissection of a major QTL for methamphetamine sensitivity implicates epistasis. Genes, Brain and Behavior 11:623-632 PDF version +Bryant CD, Kole LA, Guido MA, Sokoloff G, Palmer AA (2012) Congenic dissection of a major QTL for methamphetamine sensitivity implicates epistasis. Genes, Brain and Behavior 11:623-632 PDF version
  29. Downing C, Balderrama-Durbin C, Kimball A, Biers J, Wright H, Gilliam D, Johnson TE (2012) Quantitative trait locus mapping for ethanol teratogenesis in BXD recombinant inbred mice. Alcohol Clin Exp Res. 36:1340-1354
  30. @@ -561,7 +623,7 @@ Durrant C, Swertz MA, Alberts R, Arends D, Möller S, Mott R, Prins P, van der V
  31. Gini B, Hager R (2012) Recombinant inbred systems can advance research in behavioral ecology. Front. Gene. 3:198 Full Text version
  32. -Hager R, Lu L, Rosen GD, Williams RW. (2012) Genetic architecture supports mosaic brain evolution and independent brain-body size regulation. Nature Communications 3:1079 PDF version Full Text version +Hager R, Lu L, Rosen GD, Williams RW. (2012) Genetic architecture supports mosaic brain evolution and independent brain-body size regulation. Nature Communications 3:1079 PDF version Full Text version
  33. Jellen LC, Unger EL, Lu L, Williams RW, Rousseau S, Wang X, Earley CJ, Allen RP, Miles MF, Jones BC (2012) Systems genetic analysis of the effects of iron deficiency in mouse brain. Neurogenetics 13:147-157
  34. @@ -587,13 +649,13 @@ Talishinsky A, Rosen GD (
  35. Williams RW, Mulligan MK (2012) Genetic and molecular network analysis of behavior. Int Rev Neurobiol. 104:135-57 -PDF version +PDF version
  36. Wolen AR, Phillips CA, Langston MA, Vorster PJ, Bruce NA, York TP, Williams RW, Miles MF (2012) Genetic dissection of acute ethanol responsive gene networks in prefrontal cortex: Functional and mechanistic implications. PLoS One 7:e33575
  37. Yin L, Unger EL, Jellen LC, Earley CJ, Allen RP, Tomaszewicz A, Fleet JC, Jones BC. (2012) Systems genetic analysis of multivariate response to iron deficiency in mice. Am J Physiol Regul Integr Comp Physiol 302:R1282-96 -PDF version +PDF version
  38. Ziebarth JD, Cook MN, Wang X, Williams RW, Lu L, Cui Y (2012) Treatment- and population-dependent activity patterns of behavioral and expression QTLs. PLoS One 7:e31805. @@ -620,7 +682,7 @@ Zumbrun EE, Abdeltawab NF, Bloomfield HA, Chance TB, Nichols DK, Harrison PE, Ko -
    +
    GeneNetwork (2011)
    @@ -634,7 +696,7 @@ Alberts R, Lu L, Williams RW, Schughart K. (2011) Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease. BMC Genomics 12:610 Full Text version
  39. -Di Curzio DL, Goldowitz D (2011) The genetic basis of adrenal gland weight and structure in BXD recombinant inbred mice. Mammalian Genome 22:209–234 Full Text PDF version +Di Curzio DL, Goldowitz D (2011) The genetic basis of adrenal gland weight and structure in BXD recombinant inbred mice. Mammalian Genome 22:209–234 Full Text PDF version
  40. Gatti DM, Lu L, Williams RW, Sun W, Wright FA, Threadgill DW, Rusyn I (2011) MicroRNA expression in the livers of inbred mice. Mutation Research 714:126-133
  41. @@ -642,7 +704,7 @@ Gibson JN, Jellen LC, Unger EL, Morahan G, Mehta M, Earley CJ, Allen RP, Lu L, J
  42. Hakvoort TB, Moerland PD, Frijters R, Sokolovic A, Labruyère WT, Vermeulen JL, Ver Loren van Themaat E, Breit TM, Wittink FR, van Kampen AH, Verhoeven AJ, Lamers WH, Sokolovic M (2011) Interorgan coordination of the murine adaptive response to fasting. J Biol Chem 286:16332-43
  43. -Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372 Full Text HTML and PDF versions +Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372 Full Text HTML and PDF versions
  44. Jablonski MM, Freeman NE, Orr WE, Templeton JP, Lu L, Williams RW, Geisert EE (2011) Genetic pathways regulating glutamate levels in retinal Müller cells. Neurochem Res 36:594-603
  45. @@ -655,7 +717,7 @@ Jiao Y, Jiao F, Yan J, Xiong Q, Shriner D, Hasty K, Stuart J, Gu W (2011)) Adult hippocampal neurogenesis and plasticity in the infrapyramidal bundle of the mossy fiber projection: II. Genetic covariance and identification of Nos1 as a linking candidate gene. Frontiers in Neuroscience 5:106 PDF version -PDF +PDF
  46. Krebs J, Römer B, Overall RW, Fabel K, Babu H, Brandt MD, Williams RW, Jessberger S, Kempermann G (2011) Adult hippocampal neurogenesis and plasticity in the infrapyramidal bundle of the mossy fiber projection: II. Genetic covariation and identification of Nos1 as linking candidate gene. Frontiers in Neuroscience 5:106 PDF version @@ -676,14 +738,14 @@ Moscou MJ, Lauter N, Steffenson B, Wise RP (PDF version
  47. -Porcu P, O'Buckley TK, Song SC, Harenza JL, Lu L, Wang X, Williams RW, Miles MF, Morrow AL (2010) Genetic analysis of the neurosteroid deoxycorticosterone and its relation to alcohol phenotypes: Identification of QTLs and downstream gene regulation. PLoS One 6:e18405 Full Text HTML and PDF versions +Porcu P, O'Buckley TK, Song SC, Harenza JL, Lu L, Wang X, Williams RW, Miles MF, Morrow AL (2010) Genetic analysis of the neurosteroid deoxycorticosterone and its relation to alcohol phenotypes: Identification of QTLs and downstream gene regulation. PLoS One 6:e18405 Full Text HTML and PDF versions
  48. Sutcliffe JG, Hedlund PB, Thomas EA, Bloom FE, Hilbush BS (2011) Peripheral reduction of β-amyloid is sufficient to reduce brain β-amyloid: implications for Alzheimer's disease. J Neurosci Res. 2011 Jun;89(6):808-14. doi: 10.1002/jnr.22603 PDF version
  49. Suwanwela J, Farber CR, Haung B, Song B, Pan C, Lyon KM, Lusis AJ (2011) Systems genetics analysis of mouse chondrocyte differentiation. Journal of Bone and Mineral Research 26:74-760 -PDF version +PDF version
  50. Tan T (2011) GeneNetwork: Best of the Web. Genetics Engineering & Biotechnology News 31(3)
  51. Whitney IE, Raven MA, Lu L, Williams RW, Reese BE (2011) A QTL on chromosome 10 modulates cone photoreceptor number in the mouse retina. Invest Ophthalmol Vis Sci. 52:3228-36 @@ -701,7 +763,7 @@ Yamamoto H, Williams EG, Mouchiroud L, Cantó C, Fan W, Downes M, Héligon C, Ba -
    +
    GeneNetwork (2010)
    @@ -716,9 +778,9 @@ Ciobanu DC, Lu L, Mozhui K, Wang X, Morris JA, Taylor WL, Dietz K, Simon P, Will Downing C, Marks MJ, Larson C, Johnson TE (2010) The metabotropic glutamate receptor subtype 5 mediates sensitivity to the sedative properties of ethanol. Pharmacogenet Genomics 20:553-64
  52. Gatti DM, Zhao N, Chesler EJ, Bradford BU, Shabalin AA, Yordanova R, Lu L, Rusyn I (2010) Sex-specific gene expression in the BXD mouse liver. Physiol Genomics 42:456-68 -Full Text PDF Version +Full Text PDF Version
  53. -Grisham W, Schottler NA, Valli-Marill J, Beck L, Beatty J (2010) Teaching bioinformatics and neuroinformatics by using free web-based tools. CBE--Life Sciences Education 9: 98-107 Full Text PDF Version +Grisham W, Schottler NA, Valli-Marill J, Beck L, Beatty J (2010) Teaching bioinformatics and neuroinformatics by using free web-based tools. CBE--Life Sciences Education 9: 98-107 Full Text PDF Version
  54. Hoffman PL, Bennett B, Saba LM, Bhave SV, Carosone-Link PJ, Hornbaker CK, Kechris KJ, Williams RW, Tabakoff B 2010 Using the Phenogen website for 'in silico' analysis of morphine-induced analgesia: identifying candidate genes. Addiction Biology, doi: 10.1111/j.1369-1600.2010.00254.x
  55. @@ -728,12 +790,12 @@ Lionikas A, Carlborg O, Lu L; Peirce JL, Williams RW, Yu F, Vogler GP, McClearn
  56. Loguercio S, Overall RW, Michaelson JJ, Wiltshire T, Pletcher MT, Miller BH, Walker JR, Kempermann G, Su AI, Beyer A 2010 Integrative analysis of low- and high-resolution eQTL. PLoS One 5(11):e13920 Full Text PDF Version
  57. -Lynch RM, Naswa S, Rogers Jr GL, Kanla SA, Das S, Chesler EJ, Saxton AM, Langston MA, Voy, BH (2010) Identifying genetic loci and spleen gene coexpression networks underlying immunophenotypes in the BXD recombinant inbred mice. Physiological Genomics 41:244-253 Full Text PDF version +Lynch RM, Naswa S, Rogers Jr GL, Kanla SA, Das S, Chesler EJ, Saxton AM, Langston MA, Voy, BH (2010) Identifying genetic loci and spleen gene coexpression networks underlying immunophenotypes in the BXD recombinant inbred mice. Physiological Genomics 41:244-253 Full Text PDF version
  58. Lynch RM (2010) A systems genetics approach to the characterization of differential low dose radiation responses in the BXD recombinant inbred mice. PhD diss., University of Tennessee http://trace.tennessee.edu/utk_graddiss/727
  59. -Malkki HA, Donga LA, de Groot SE, Battaglia FP; NeuroBSIK Mouse Phenomics Consortium, Pennartz CM (2010) Appetitive operant conditioning in mice: heritability and dissociability of training stages. Front Behav Neuroscience 4:171 Full Text PDF version +Malkki HA, Donga LA, de Groot SE, Battaglia FP; NeuroBSIK Mouse Phenomics Consortium, Pennartz CM (2010) Appetitive operant conditioning in mice: heritability and dissociability of training stages. Front Behav Neuroscience 4:171 Full Text PDF version
  60. -Mulligan MK, Lu L, Overall RW, Kempermann G, Rogers GL, Langston MA, Williams RW (2010) Genetic analysis of BDNF expression cliques and adult neurogenesis in the hippocampus. Biomedical Sciences and Engineering Conference (BSEC) DOI: 10.1109/BSEC.2010.5510848 Full Text PDF version +Mulligan MK, Lu L, Overall RW, Kempermann G, Rogers GL, Langston MA, Williams RW (2010) Genetic analysis of BDNF expression cliques and adult neurogenesis in the hippocampus. Biomedical Sciences and Engineering Conference (BSEC) DOI: 10.1109/BSEC.2010.5510848 Full Text PDF version
  61. Peidis P, Giannakouros T, Burow ME, Williams RW, Scott RE (2010) Systems genetics analyses predict a transcription role for P2P-R: molecular confirmation that P2P-R is a transcriptional co-repressor. BMC Systems Biology 4:14 Full Text PDF version and
  62. @@ -743,7 +805,7 @@ Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska KJ, Rosen GD, Lu L, Kullander
  63. Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV (2010) Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. Genes, Brain and Behavior 5:257-73. Full Text HTML Version
  64. -Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ (2010) Systems genetics analysis of mouse chondrocyte differentiation. JBMR, in press Full Text PDF version +Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ (2010) Systems genetics analysis of mouse chondrocyte differentiation. JBMR, in press Full Text PDF version
  65. Wang X, Chen Y, Wang X, Lu L. (2010) Genetic regulatory network analysis for App based on genetical genomics approach. Exp Aging Res 36:79-93 @@ -766,7 +828,7 @@ Wang X, Chen Y, Wang X, Lu L. ( +
    GeneNetwork (2009)
    @@ -776,7 +838,7 @@ Wang X, Chen Y, Wang X, Lu L. (2009) Genetic dissection of the mouse brain using high-field magnetic resonance microscopy. Neuroimaging 45:1067-79
  66. -Boon AC, deBeauchamp J, Hollmann A, Luke J, Kotb M, Rowe S, Finkelstein D, Neale G, Lu L, Williams RW, Webby RJ (2009) Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice. J Virol 83:10417-26 PMID: 19706712 Full Text PDF Version +Boon AC, deBeauchamp J, Hollmann A, Luke J, Kotb M, Rowe S, Finkelstein D, Neale G, Lu L, Williams RW, Webby RJ (2009) Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice. J Virol 83:10417-26 PMID: 19706712 Full Text PDF Version
  67. Brigman JL, Mathur P, Lu L, Williams RW, Holmes A (2009) Genetic relationship between anxiety- and fear-related behaviors in BXD recombinant inbred mice. Behavioral Pharmacology 20:204-209 Full Text HTML Version, @@ -836,7 +898,7 @@ Silva GL, Junta CM, Sakamoto-Hojo ET, Donadi EA, Louzada-Junior P, Passos GA (2009) Identification of candidate genes and gene networks specifically associated with analgesic tolerance to morphine. J Neurosci 2:5295-307 Full Text HTML
  68. Thomas C, Gioiello A, Noriega L, Strehle A, Oury J, Rizzo G, Macchiarulo A, Yamamoto H, Mataki C, Pruzanski M, Pellicciari R, Auwerx J, Schoonjans K (2009) TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab 10:167-77 -Full Text PDF +Full Text PDF
  69. Webb BT, McClay JL, Vargas-Irwin C, York TP, van den Oord EJCG (2009) In silico whole genome association scan for murine prepulse inhibition. PLoS ONE 4: e5246. doi:10.1371/journal.pone.0005246 Full Text HTML, @@ -856,7 +918,7 @@ Zheng QY, Ding D, Yu H, Salvi RJ, Johnson KR ( +
    GeneNetwork (2008)
    @@ -928,7 +990,7 @@ Hayat Y, Yang J, Xu HM, Zhu J (2008) Genetic control of experience-dependent plasticity in the visual cortex. Genes Brain Behav 7:915-23. -Full Text PDF Version +Full Text PDF Version
  70. Jan TA, Lu L, Li CX, Williams RW, Waters RS (2008) Genetic analysis of posterior medial barrel subfield (PMBSF) size in somatosensory cortex (SI) in recombinant inbred strains of mice. BMC Neuroscience 9:3 Full Text PDF Version @@ -941,7 +1003,7 @@ Jones LC, Beard JL, Jones BC (2008) Of mice and men, periodic limb movements and iron: how the human genome informs the mouse genome. Genes, Brain and Behavior 7:513-514. -Full Text PDF Version +Full Text PDF Version
  71. Kang HM, Ye C, Eskin E (2008) Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics doi:10.1534/genetics.108.094201 @@ -949,7 +1011,7 @@ Kang HM, Ye C, Eskin E (2008) Genetical systems biology in livestock: Application to gonadotrophin releasing hormone and reproduction. IET Systems Biology 2:423-441 -Full Text PDF Version +Full Text PDF Version
  72. Kerns RT, Miles MF (2008) Microarray analysis of ethanol-induced changes in gene expression. Alcohol: Methods and Protocols. In: Methods in Molecular Biology 447:395-410 Full Text PDF Version @@ -970,7 +1032,7 @@ Macedo C, Magalhaes DA, Tonani M, Marques MC, Junta CM, Passos GA (Full Text PDF Version +Full Text PDF Version
  73. Mozhui RT, Ciobanu DC, Schikorski T, Wang XS, Lu L, Williams RW (2008) Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression. PLoS Genetics 4: e1000260. doi:10.1371/journal.pgen.1000260 Full Text HTML Version @@ -1007,7 +1069,7 @@ Zhang Y, Maksakova IA, Gagnier L , van de Lagemaat LN, Mager DL (2008) Genome-wi -
    +
    GeneNetwork (2007)
    @@ -1051,7 +1113,7 @@ Fox JG, Barthold SW, Davisson MT, Newcomer CE (2007) Informatics in neuroscience. Briefings in Bioinformatics 8:446-456
  74. Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I (2007) Genome-level analysis of genetic regulation of liver gene expression networks. Hepatology 46:548-557 - Full Text PDF Version + Full Text PDF Version
  75. Grice DE, Reenila I, Mannisto PT, Brooks Ai, Smith GG, Golden GT, Buxbaum JD, Berrettini WH (2007) Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine. BMC Genomics 8:76 Full Text PDF Version, @@ -1073,12 +1135,12 @@ Jawad M, Giotopoulos G, Fitch S, Cole C, Plumb M, Talbot CJ (2007) ZOOMING IN: a new high-resolution gene expression atlas of the brain. Mol Syst Biol. 3:75
  76. Jones BC, Beard JL, Gibson JN, Unger EL, Allen RP, McCarthy KA, Earley CJ (2007) Systems genetic analysis of peripheral iron parameters in the mouse. American Journal of Physiology Regul Integr Comp Physiol 293: R116-124 -Full Text HTML Version, and see full text of Jones et al., 1999. +Full Text HTML Version, and see full text of Jones et al., 1999.
  77. Jones BC and Mormede JP (2007) Neurobehavioral genetics: methods and applications. (2007)" CRC Press, Taylor & Francis Group, Boca Raton, Florida, p. 102, ISBN 084931903X
  78. Kadarmideen HN, Reverter A (2007) Combined genetic, genomic and transcriptomic methods in the analysis of animal traits. CABI Review: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 2: No. 042 (16 pp) -Full Text PDF Version +Full Text PDF Version
  79. Korostynski M, Piechota M, Kaminska D, Solecki W. Przewlocki R (2007) Morphine effects on striatal transcriptome in mice. Genome Biology 8:R128
  80. @@ -1097,7 +1159,7 @@ Mouse Phenotype Database Integration Consortium (2007) The p47 GTPases Iigp2 and Irgb10 regulate innate immunity and inflammation to murine Chlamydia psittaci. J Immunol 179:1814-1824
  81. Mozhui K, Hamre KM, Holmes A, Lu L, Williams RW (2007) Genetic and structural analysis of the basolateral amygdala complex in BXD recombinant inbred mice. Behav Genet. 37:223-243 -Full Text MS Word Version (authors' copy) +Full Text MS Word Version (authors' copy)
  82. Peirce JL, Broman KW, Lu L, Williams RW (2007) A simple method for combining genetic mapping data from multiple crosses and experimental designs. PLoS ONE 2:e1036 Full Text PDF Version, @@ -1123,10 +1185,10 @@ Taylor M, Valdar W, Kumar A, Flint J, Mott R (Full Text HTML Version
  83. Vazquez-Chona F, Lu L, Williams RW, Geisert EE (2007) Genetic influences on retinal gene expression and wound healing. Gene Regulation and Systems Biology 1:327-348 -Full Text PDF Version +Full Text PDF Version
  84. von Rohr P, Friberg M, Kadarmideen HN (2007) Prediction of transcription factor binding sites using results from genetical genomics investigations. Journal of Bioinformatics and Computational Biology 5:773-793 -Full Text PDF Version +Full Text PDF Version
  85. Wan X, Pavlidis P (2007) Sharing and reusing gene expression profiling data in neuroscience. Neuroinformatics 5:161-75. HTML example of using GEMMA and GeneNetwork. @@ -1138,7 +1200,7 @@ Zou W, Aylor DL, Zeng ZB ( -
    +
    GeneNetwork (2006)
    @@ -1231,7 +1293,7 @@ Williams RW ( +
    GeneNetwork (2005)
    @@ -1256,7 +1318,7 @@ Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Inferring gene transcriptional modulatory relations: a genetical genomics approach. Human Molecular Genetics 14: 1119-1125
  86. Li J, Burmeister M (2005) Genetical genomics: combining genetics with gene expression analysis. Human Molecular Genetics 14:163-169. - [ Full text PDF version] + [ Full text PDF version]
  87. Lozier JN, Tayebi N, Zhang P (2005) Mapping of genes that control the antibody response to human factor IX in mice. Blood 105: 1029-1035 @@ -1268,7 +1330,7 @@ MacLaren EJ, Sikela JM (2005) Complex genetics of interactions of alcohol and CNS function and behavior. Alcoholism: Clinical and Experimental Research 29:1706-1719
  88. Mountz JD, Yang P, Wu Q, Zhou J, Tousson A, Fitzgerald A, Allen J, Wang X, Cartner S, Grizzle WE, Yi N, Lu L, Williams RW, Hsu HC (2005) Genetic segregation of spontaneous erosive arthritis and generalized autoimmune disease in BXD2 recombinant inbred strain of mice. Scadinavian Journal of Immunology 61:1-11 -Full Text PDF Version +Full Text PDF Version
  89. Li CX, Wei X, Lu L, Peirce JL, Wiliams RW, Waters RS (2005) Genetic analysis of barrel field size in the first somatosensory area (S1) in inbred and recombinant inbred strains of mice. Somatosensory and Motor Research 22:141-150
  90. @@ -1294,7 +1356,7 @@ Yang H, Crawford N, Lukes L, Finney R, Lancaster M, Hunter KW ( +
    GeneNetwork (2004)
    @@ -1348,7 +1410,7 @@ Zareparsi S, Hero A, Zack DJ, Williams RW, Swaroop A ( +
    GeneNetwork (2003)
    @@ -1381,51 +1443,49 @@ Rosen GD, La Porte NT, Diechtiareff B, Pung, CJ, Nissanov J, Gustafson C, Bertra
    -
    Background references on inbred strains and other key resources

    +
    Background references on inbred strains and other key resources - -11737945 -
    +
    Williams RW, Gu J, Qi S, Lu L (2001) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biology 2:46.1–46.18 Full Text HTML and PDF Version. [General background on recombinant inbred strains.]
    -
    +
    Peirce JL, Lu L, Gu J, Silver LM, Williams RW (2004) A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genetics 5:7 Full Text PDF Version. [Background on the expanded set of BXD strains.]
    -
    +
    Williams RW, Bennett B, Lu L, Gu J, DeFries JC, Carosone-Link PJ, Rikke BA, Belknap JK, Johnson TE (2004) Genetic structure of the LXS panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis. Mammalian Genome 15:637-647 [Background on origins and the genetic structure large panel of LXS strains. Please cite this paper is you have used LXS data sets.]
    -
    +
    Grubb SC, Churchill GA, Bogue MA (2004) A collaborative database of inbred mouse strain characteristics. Bioinformatics 20:2857-2859 [One of two key papers on the Mouse Phenome Project and database at The Jackson Laboratory. The mouse diversity panel (MDP) is a superset of strains that are part of the Phenome Project. Full Text PDF Version.]
    -
    +
    Bogue MA, Grubb SC (2004) The mouse phenome project. Genetica 122:71-74 [One of two key papers on the Mouse Phenome Project and database at The Jackson Laboratory. The mouse diversity panel (MDP) is a superset of strains that are part of the Phenome Project. Please contact Dr. Molly Bogue for information on the Phenome Project: mollyb@jax.org]
    -
    +
    Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, Gupta RV, Montgomery J, Morenzoni MM, Nilsen GB, Pethiyagoda CL, Stuve LL, Johnson FM, Daly MJ, Wade CM, Cox DR (2007) A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448, 1050-3
    -
    +
    Loudet O, Chaillou S, Camilleri C, Bouchez D, Daniel-Vedele F (2002) Bay-0 x Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis. Theoretical and Applied Genetics 104:1173-1184 Full Text PDF Version [Please cite this paper is you have used the BXS Arabidopsis data sets.]
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    +
    Jirout M, Krenova D, Kren V, Breen L, Pravenec M, Schork NJ, Printz MP (2003) A new framework marker-based linkage map and SDPs for the rat HXB/BXH strain set. expression differences in mice diverently selected for methamphetamine sensitivity. Mammalian Genome 14: 537-546
    -
    +
    Shifman S, Bell JT, Copley BR, Taylor M, Williams RW, Mott R, Flint J (2006) A high resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biology 4:2227-2237 Full Text PDF Version [A comprehensive analysis of recombination rates using several populations of mice, including most major GRPs.]
    Information about this HTML page:

    -
    +

    This text originally generated by RWW, April 2003. Updated by RWW, Oct 15, Dec 17, 2004; RWW Jan 19, 2005; EJC Mar 9; RWW Mar 29, Apr 15; RWW Jan 7, 2006, Jan 21, July 26, Aug 26, 2006s; May 2007; Feb 2008; March 19 2008

    @@ -1433,4 +1493,5 @@ Shifman S, Bell JT, Copley BR, Taylor M, Williams RW, Mott R, Flint J ( -

    You entered at least one incorrect search command.

    +

    You entered at least one incorrect search command, or your search term was not applicable to the dataset type.

    +

    Some search terms may not be applicable to Phenotype or Genotype datasets (RIF, etc)

    diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index abd487ec..09f36021 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -68,46 +68,111 @@ {% endif %} {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %} - {% if this_trait.dataset.type != 'Publish' %} Resource Links - {% if this_trait.pubmed_id %} -     + {% if pubmed_link %} + PubMed {% endif %} - {% if this_trait.geneid %} - - NCBI + {% if ncbi_gene_link %} + + Gene    {% endif %} - {% if this_trait.omim %} - + {% if omim_link %} + OMIM    {% endif %} + {% if unigene_link %} + + UniGene + +    + {% endif %} + {% if genbank_link %} + + GenBank + +    + {% endif %} + {% if homologene_link %} + + HomoloGene + +    + {% endif %} {% if this_trait.symbol %} - + Genotation    - + GTEx Portal    - {% if (dataset.group.species == "mouse" or dataset.group.species == "human") and this_trait.symbol %} - + {% if genebridge_link %} + GeneBridge {% endif %} - {% endif %} + {% endif %} +
    + {% if ucsc_blat_link %} + + UCSC + +    + {% endif %} + {% if biogps_link %} + + BioGPS + +    + {% endif %} + {% if string_link %} + + STRING + +    + {% endif %} + {% if panther_link %} + + PANTHER + +    + {% endif %} + {% if gemma_link %} + + Gemma + +    + {% endif %} + {% if aba_link %} + + ABA + +    + {% endif %} + {% if ebi_gwas_link %} + + EBI GWAS + +    + {% endif %} + {% if wiki_pi_link %} + + Wiki-Pi + +    + {% endif %} {% endif %} - {% endif %}
    -- cgit v1.2.3