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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.293702425885355,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.137330689990864,0.162956623790281,0.19051105458665,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.409444531957759,0.364494238865932,0,0,0,0,0,0,0,0,0,0,0,0,0.358592398801571,0.326322748905698,0.379520168325414,0.0317017435824471,0.0158196551188907,0,0,0,0,0,0,0.17315756550851,0,0,0,0,0,0,0,0,0,0,0.251573973943328,0,0.276611790108454,0.303455666003353,0.244171184123748,0.224288318617122,0.312824185754616,0.167422152083431,0.276932470934985,0,0,0,0.275998746730683,0.153713679451033,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.542299843337517,0.619956193281725,0.944922148764837,0,0,0,0,0.0304819657131131,0,0,0,0,0.21661553485341,0.289038021474128,0.184081677162945,0.362628448947527,0.149291438599461,0.408447316132326,0.258032988669288,0.500296565492842,0,0,0,0,0,0,0,0,0.0202767701688924,0,0,0,0,0,0.0338533374824575,0,0,0,0,0,0,0,0.211103171726276,0.114803811732104,0.141951942539884,0.0797901069290224,0.154588041779746,0.168053962823626,0,0.0662136857075299,0.0973736644748266,0.203269403191864,0.110173605842676,0,0.0849828766602549,0.0394351756113673,0.488623114446615,0.499002269726579,0.711150377839304,0.653790779153302,0.726422247559149,0.729296227248365,0.871772197194119,0.66291599793211,0.748436349140669,0.786128627671199,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0321269055488328,0,0,0,0,0,0.0646317955501215,0.289492325791132,0,0,0.278724990286798,0.269911672981586,0,0,0,0,0,0,0.07380890348825,0.055674254769948,0,0,0.281211900833848,0.455945446105409,0.405879528568754,0.328253357621743,0,0,0.114718896326828,0.0750375819757342,0.053672552146501,0.162278901062865,0.0063848288646406,0,0.225235044503296,0.0596340098159245,0,0,0,0,0,0,0,0,0,0,0.12933740395509,0.148545992280576,0.0432739443039237,0.12041278578576,0.207867562319602,0.3553694089625,0.371795377437702,0.217065655592723,0.0555439831843405,0.217609945927666,0,0.0814866010703366,0.0582376243470695,0,0,0,0,0,0,0,0.0318857800356453,0.0803809427109337,0.0647396218295386,0.0824580172145032,0.0951219240511376,0.103710933695783,0,0,0.199190130896582,0,0,0.458852625634775,0.490512521457896,0.557908558770813,0.583466851599692,0.573026121560612,0.457598508734129,0.505544173173409,0.223810833220367,0.0469880747817416,0.109925980570702,0.059629779596053,0,0,0.0265240061007451,0.00926081617910975,0,0,0,0.0255436553954063,0.031895734489288,0,0.0201939307380272,0.0199472445765722,0,0,0,0,0,0.332534871232516,0.485544638919422,0.321098994686378,0.0843504501108034,0.350235379900689,0,0,0,0,0,0,0,0,0,0,0.224884155443985,0.145825435924841,0.179609468438842,0.0945084131504676,0.0826465040380816,0.073294297058821,0.154513394593269,0.235032483595276,0.168103334988355,0.17765030293269,0.098117166361508,0.19158416385364,0.206282881471566,0.247556396095555,0.295692035921412,0.169172763866184,0.165403796547116,0.195040524486061,0.14986111676545,0.233211892786115,0.128033729919821,0.182447658702885,0.201842612947909,0.207810139456627,0.153117691777992,0.164315199042335,0.155716970477612,0.18359421108913,0.206741431078382,0.163401805547804,0.217859547129108,0.227026872602678,0.074491100723522,0.332337228780856,0.184932892993548,0.136412877324794,0.258875589736247,0.216063761676531,0.193735829136543,0.363261960472786,0.234590645853713
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|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00774099031919663;15436,15437!GO:0005667;transcription factor complex;0.00774099031919663;15436,15437!GO:0043565;sequence-specific DNA binding;0.00774099031919663;15436,15437!GO:0009887;organ morphogenesis;0.00774099031919663;15436,15437!GO:0044451;nucleoplasm part;0.00774099031919663;15436,15437!GO:0005654;nucleoplasm;0.00774099031919663;15436,15437!GO:0031981;nuclear lumen;0.00927992739384473;15436,15437!GO:0031974;membrane-enclosed lumen;0.00927992739384473;15436,15437!GO:0043233;organelle lumen;0.00927992739384473;15436,15437!GO:0003700;transcription factor activity;0.0100769759894287;15436,15437!GO:0044428;nuclear part;0.0134197692955157;15436,15437!GO:0009653;anatomical structure morphogenesis;0.0159826463630404;15436,15437!GO:0048513;organ development;0.0209993850407017;15436,15437!GO:0043234;protein complex;0.0249859407258191;15436,15437!GO:0048731;system development;0.0249859407258191;15436,15437!GO:0006355;regulation of transcription, DNA-dependent;0.0249859407258191;15436,15437!GO:0006351;transcription, DNA-dependent;0.0249859407258191;15436,15437!GO:0032774;RNA biosynthetic process;0.0249859407258191;15436,15437!GO:0003677;DNA binding;0.0249859407258191;15436,15437!GO:0045449;regulation of transcription;0.0249859407258191;15436,15437!GO:0048856;anatomical structure development;0.0249859407258191;15436,15437!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0249859407258191;15436,15437!GO:0006350;transcription;0.0249859407258191;15436,15437!GO:0032991;macromolecular complex;0.0249859407258191;15436,15437!GO:0010468;regulation of gene expression;0.0249859407258191;15436,15437!GO:0031323;regulation of cellular metabolic process;0.0259960277491642;15436,15437!GO:0007275;multicellular organismal development;0.0259960277491642;15436,15437!GO:0019222;regulation of metabolic process;0.0259960277491642;15436,15437!GO:0016070;RNA metabolic process;0.0264421083823468;15436,15437!GO:0044446;intracellular organelle part;0.0265077605788722;15436,15437!GO:0044422;organelle part;0.0265077605788722;15436,15437!GO:0010467;gene expression;0.0343177985962733;15436,15437!GO:0003676;nucleic acid binding;0.0349031074208671;15436,15437!GO:0032502;developmental process;0.0360811872666491;15436,15437!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0382194453525193;15436,15437!GO:0050794;regulation of cellular process;0.0427343490279872;15436,15437!
|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00774099031919663;15436,15437!GO:0005667;transcription factor complex;0.00774099031919663;15436,15437!GO:0043565;sequence-specific DNA binding;0.00774099031919663;15436,15437!GO:0009887;organ morphogenesis;0.00774099031919663;15436,15437!GO:0044451;nucleoplasm part;0.00774099031919663;15436,15437!GO:0005654;nucleoplasm;0.00774099031919663;15436,15437!GO:0031981;nuclear lumen;0.00927992739384473;15436,15437!GO:0031974;membrane-enclosed lumen;0.00927992739384473;15436,15437!GO:0043233;organelle lumen;0.00927992739384473;15436,15437!GO:0003700;transcription factor activity;0.0100769759894287;15436,15437!GO:0044428;nuclear part;0.0134197692955157;15436,15437!GO:0009653;anatomical structure morphogenesis;0.0159826463630404;15436,15437!GO:0048513;organ development;0.0209993850407017;15436,15437!GO:0043234;protein complex;0.0249859407258191;15436,15437!GO:0048731;system development;0.0249859407258191;15436,15437!GO:0006355;regulation of transcription, DNA-dependent;0.0249859407258191;15436,15437!GO:0006351;transcription, DNA-dependent;0.0249859407258191;15436,15437!GO:0032774;RNA biosynthetic process;0.0249859407258191;15436,15437!GO:0003677;DNA binding;0.0249859407258191;15436,15437!GO:0045449;regulation of transcription;0.0249859407258191;15436,15437!GO:0048856;anatomical structure development;0.0249859407258191;15436,15437!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0249859407258191;15436,15437!GO:0006350;transcription;0.0249859407258191;15436,15437!GO:0032991;macromolecular complex;0.0249859407258191;15436,15437!GO:0010468;regulation of gene expression;0.0249859407258191;15436,15437!GO:0031323;regulation of cellular metabolic process;0.0259960277491642;15436,15437!GO:0007275;multicellular organismal development;0.0259960277491642;15436,15437!GO:0019222;regulation of metabolic process;0.0259960277491642;15436,15437!GO:0016070;RNA metabolic process;0.0264421083823468;15436,15437!GO:0044446;intracellular organelle part;0.0265077605788722;15436,15437!GO:0044422;organelle part;0.0265077605788722;15436,15437!GO:0010467;gene expression;0.0343177985962733;15436,15437!GO:0003676;nucleic acid binding;0.0349031074208671;15436,15437!GO:0032502;developmental process;0.0360811872666491;15436,15437!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0382194453525193;15436,15437!GO:0050794;regulation of cellular process;0.0427343490279872;15436,15437!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000489!4.65e-17!21;UBERON:0005156!1.07e-13!26;UBERON:0000990!1.07e-13!26;UBERON:0006554!3.29e-13!18;UBERON:0003133!3.59e-13!24;UBERON:0001008!3.61e-13!19;UBERON:0002113!8.74e-13!14;UBERON:0003918!8.74e-13!14;UBERON:0011143!8.74e-13!14;UBERON:0005095!8.74e-13!14;UBERON:0007687!8.74e-13!14;UBERON:0000991!1.04e-10!18;UBERON:0005564!1.04e-10!18;UBERON:0004176!5.77e-10!17;UBERON:0009196!5.77e-10!17;UBERON:0009117!5.77e-10!17;UBERON:0003135!6.63e-09!15;UBERON:0003101!8.39e-09!16;UBERON:0000079!8.39e-09!16;UBERON:0003064!3.48e-08!14;UBERON:0000473!4.50e-08!14;UBERON:0003886!2.78e-07!38;UBERON:0002553!7.36e-07!39
}}
}}

Revision as of 16:54, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr2:74542918..74542971,+p1@Hoxd8
Mm9::chr2:74542974..74542986,+p5@Hoxd8
Mm9::chr2:74543103..74543135,+p4@Hoxd8
Mm9::chr2:74543202..74543213,+p3@Hoxd8
Mm9::chr2:74543235..74543246,+p7@Hoxd8
Mm9::chr2:74560109..74560131,+p1@Hoxd4


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0007389pattern specification process0.00774099031919663
GO:0005667transcription factor complex0.00774099031919663
GO:0043565sequence-specific DNA binding0.00774099031919663
GO:0009887organ morphogenesis0.00774099031919663
GO:0044451nucleoplasm part0.00774099031919663
GO:0005654nucleoplasm0.00774099031919663
GO:0031981nuclear lumen0.00927992739384473
GO:0031974membrane-enclosed lumen0.00927992739384473
GO:0043233organelle lumen0.00927992739384473
GO:0003700transcription factor activity0.0100769759894287
GO:0044428nuclear part0.0134197692955157
GO:0009653anatomical structure morphogenesis0.0159826463630404
GO:0048513organ development0.0209993850407017
GO:0043234protein complex0.0249859407258191
GO:0048731system development0.0249859407258191
GO:0006355regulation of transcription, DNA-dependent0.0249859407258191
GO:0006351transcription, DNA-dependent0.0249859407258191
GO:0032774RNA biosynthetic process0.0249859407258191
GO:0003677DNA binding0.0249859407258191
GO:0045449regulation of transcription0.0249859407258191
GO:0048856anatomical structure development0.0249859407258191
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0249859407258191
GO:0006350transcription0.0249859407258191
GO:0032991macromolecular complex0.0249859407258191
GO:0010468regulation of gene expression0.0249859407258191
GO:0031323regulation of cellular metabolic process0.0259960277491642
GO:0007275multicellular organismal development0.0259960277491642
GO:0019222regulation of metabolic process0.0259960277491642
GO:0016070RNA metabolic process0.0264421083823468
GO:0044446intracellular organelle part0.0265077605788722
GO:0044422organelle part0.0265077605788722
GO:0010467gene expression0.0343177985962733
GO:0003676nucleic acid binding0.0349031074208671
GO:0032502developmental process0.0360811872666491
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0382194453525193
GO:0050794regulation of cellular process0.0427343490279872



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
cavitated compound organ4.65e-1721
reproductive structure1.07e-1326
reproductive system1.07e-1326
urinary system structure3.29e-1318
reproductive organ3.59e-1324
renal system3.61e-1319
kidney8.74e-1314
kidney mesenchyme8.74e-1314
upper urinary tract8.74e-1314
kidney rudiment8.74e-1314
kidney field8.74e-1314
gonad1.04e-1018
gonad primordium1.04e-1018
external genitalia5.77e-1017
indifferent external genitalia5.77e-1017
indifferent gonad5.77e-1017
male reproductive organ6.63e-0915
male organism8.39e-0916
male reproductive system8.39e-0916
intermediate mesoderm3.48e-0814
testis4.50e-0814
body cavity precursor2.78e-0738
anatomical cavity7.36e-0739


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}

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