diff options
Diffstat (limited to 'wqflask')
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;"> 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> 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 (<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> Spearman Rank <input type="radio" name= - "tissue_method" value="5"><br> + Pearson <input type="radio" name="sample_method" value="pearson" checked> 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 (<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> |