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|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.0081875859145349;15436,15434!GO:0005667;transcription factor complex;0.0081875859145349;15436,15434!GO:0043565;sequence-specific DNA binding;0.0081875859145349;15436,15434!GO:0009887;organ morphogenesis;0.0081875859145349;15436,15434!GO:0044451;nucleoplasm part;0.0081875859145349;15436,15434!GO:0005654;nucleoplasm;0.0081875859145349;15436,15434!GO:0030878;thyroid gland development;0.00860702973948846;15434!GO:0031981;nuclear lumen;0.00867856041821122;15436,15434!GO:0031974;membrane-enclosed lumen;0.00883377703837142;15436,15434!GO:0043233;organelle lumen;0.00883377703837142;15436,15434!GO:0003700;transcription factor activity;0.00968939998983532;15436,15434!GO:0044428;nuclear part;0.0130111545252997;15436,15434!GO:0009653;anatomical structure morphogenesis;0.0156043588751578;15436,15434!GO:0048513;organ development;0.0192596718015089;15436,15434!GO:0035270;endocrine system development;0.0192596718015089;15434!GO:0043234;protein complex;0.0235490566303766;15436,15434!GO:0048731;system development;0.0235490566303766;15436,15434!GO:0048732;gland development;0.0235490566303766;15434!GO:0006355;regulation of transcription, DNA-dependent;0.0235490566303766;15436,15434!GO:0006351;transcription, DNA-dependent;0.0235490566303766;15436,15434!GO:0032774;RNA biosynthetic process;0.0235490566303766;15436,15434!GO:0003677;DNA binding;0.0235490566303766;15436,15434!GO:0045449;regulation of transcription;0.0235490566303766;15436,15434!GO:0048856;anatomical structure development;0.0235490566303766;15436,15434!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0235490566303766;15436,15434!GO:0006350;transcription;0.0235490566303766;15436,15434!GO:0032991;macromolecular complex;0.0235490566303766;15436,15434!GO:0010468;regulation of gene expression;0.0235959261662096;15436,15434!GO:0031323;regulation of cellular metabolic process;0.0246882310297342;15436,15434!GO:0007275;multicellular organismal development;0.0248349148472164;15436,15434!GO:0019222;regulation of metabolic process;0.0248349148472164;15436,15434!GO:0016070;RNA metabolic process;0.0253456507631269;15436,15434!GO:0044446;intracellular organelle part;0.0255631967120911;15436,15434!GO:0044422;organelle part;0.0255631967120911;15436,15434!GO:0010467;gene expression;0.033186442598594;15436,15434!GO:0003676;nucleic acid binding;0.0338403525474753;15436,15434!GO:0032502;developmental process;0.035068513611556;15436,15434!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0372330122993926;15436,15434!GO:0050794;regulation of cellular process;0.041722885145668;15436,15434!
|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.0081875859145349;15436,15434!GO:0005667;transcription factor complex;0.0081875859145349;15436,15434!GO:0043565;sequence-specific DNA binding;0.0081875859145349;15436,15434!GO:0009887;organ morphogenesis;0.0081875859145349;15436,15434!GO:0044451;nucleoplasm part;0.0081875859145349;15436,15434!GO:0005654;nucleoplasm;0.0081875859145349;15436,15434!GO:0030878;thyroid gland development;0.00860702973948846;15434!GO:0031981;nuclear lumen;0.00867856041821122;15436,15434!GO:0031974;membrane-enclosed lumen;0.00883377703837142;15436,15434!GO:0043233;organelle lumen;0.00883377703837142;15436,15434!GO:0003700;transcription factor activity;0.00968939998983532;15436,15434!GO:0044428;nuclear part;0.0130111545252997;15436,15434!GO:0009653;anatomical structure morphogenesis;0.0156043588751578;15436,15434!GO:0048513;organ development;0.0192596718015089;15436,15434!GO:0035270;endocrine system development;0.0192596718015089;15434!GO:0043234;protein complex;0.0235490566303766;15436,15434!GO:0048731;system development;0.0235490566303766;15436,15434!GO:0048732;gland development;0.0235490566303766;15434!GO:0006355;regulation of transcription, DNA-dependent;0.0235490566303766;15436,15434!GO:0006351;transcription, DNA-dependent;0.0235490566303766;15436,15434!GO:0032774;RNA biosynthetic process;0.0235490566303766;15436,15434!GO:0003677;DNA binding;0.0235490566303766;15436,15434!GO:0045449;regulation of transcription;0.0235490566303766;15436,15434!GO:0048856;anatomical structure development;0.0235490566303766;15436,15434!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0235490566303766;15436,15434!GO:0006350;transcription;0.0235490566303766;15436,15434!GO:0032991;macromolecular complex;0.0235490566303766;15436,15434!GO:0010468;regulation of gene expression;0.0235959261662096;15436,15434!GO:0031323;regulation of cellular metabolic process;0.0246882310297342;15436,15434!GO:0007275;multicellular organismal development;0.0248349148472164;15436,15434!GO:0019222;regulation of metabolic process;0.0248349148472164;15436,15434!GO:0016070;RNA metabolic process;0.0253456507631269;15436,15434!GO:0044446;intracellular organelle part;0.0255631967120911;15436,15434!GO:0044422;organelle part;0.0255631967120911;15436,15434!GO:0010467;gene expression;0.033186442598594;15436,15434!GO:0003676;nucleic acid binding;0.0338403525474753;15436,15434!GO:0032502;developmental process;0.035068513611556;15436,15434!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0372330122993926;15436,15434!GO:0050794;regulation of cellular process;0.041722885145668;15436,15434!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000489!8.08e-16!21;UBERON:0005156!5.36e-15!26;UBERON:0000990!5.36e-15!26;UBERON:0003133!6.47e-14!24;UBERON:0001008!8.21e-13!19;UBERON:0006554!1.26e-12!18;UBERON:0002113!3.64e-11!14;UBERON:0003918!3.64e-11!14;UBERON:0011143!3.64e-11!14;UBERON:0005095!3.64e-11!14;UBERON:0007687!3.64e-11!14;UBERON:0000991!7.90e-11!18;UBERON:0005564!7.90e-11!18;UBERON:0004176!3.13e-10!17;UBERON:0009196!3.13e-10!17;UBERON:0009117!3.13e-10!17;UBERON:0003101!4.27e-09!16;UBERON:0000079!4.27e-09!16;UBERON:0003135!7.79e-09!15;UBERON:0003064!1.84e-08!14;UBERON:0000473!4.68e-08!14
}}
}}

Revision as of 18:19, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr2:74543872..74543890,-p@chr2:74543872..74543890
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Mm9::chr2:74549915..74549930,+p6@Hoxd3
Mm9::chr2:74549945..74549965,+p4@Hoxd3
Mm9::chr2:74550178..74550214,+p5@Hoxd3


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 process0.0081875859145349
GO:0005667transcription factor complex0.0081875859145349
GO:0043565sequence-specific DNA binding0.0081875859145349
GO:0009887organ morphogenesis0.0081875859145349
GO:0044451nucleoplasm part0.0081875859145349
GO:0005654nucleoplasm0.0081875859145349
GO:0030878thyroid gland development0.00860702973948846
GO:0031981nuclear lumen0.00867856041821122
GO:0031974membrane-enclosed lumen0.00883377703837142
GO:0043233organelle lumen0.00883377703837142
GO:0003700transcription factor activity0.00968939998983532
GO:0044428nuclear part0.0130111545252997
GO:0009653anatomical structure morphogenesis0.0156043588751578
GO:0048513organ development0.0192596718015089
GO:0035270endocrine system development0.0192596718015089
GO:0043234protein complex0.0235490566303766
GO:0048731system development0.0235490566303766
GO:0048732gland development0.0235490566303766
GO:0006355regulation of transcription, DNA-dependent0.0235490566303766
GO:0006351transcription, DNA-dependent0.0235490566303766
GO:0032774RNA biosynthetic process0.0235490566303766
GO:0003677DNA binding0.0235490566303766
GO:0045449regulation of transcription0.0235490566303766
GO:0048856anatomical structure development0.0235490566303766
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0235490566303766
GO:0006350transcription0.0235490566303766
GO:0032991macromolecular complex0.0235490566303766
GO:0010468regulation of gene expression0.0235959261662096
GO:0031323regulation of cellular metabolic process0.0246882310297342
GO:0007275multicellular organismal development0.0248349148472164
GO:0019222regulation of metabolic process0.0248349148472164
GO:0016070RNA metabolic process0.0253456507631269
GO:0044446intracellular organelle part0.0255631967120911
GO:0044422organelle part0.0255631967120911
GO:0010467gene expression0.033186442598594
GO:0003676nucleic acid binding0.0338403525474753
GO:0032502developmental process0.035068513611556
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0372330122993926
GO:0050794regulation of cellular process0.041722885145668



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 organ8.08e-1621
reproductive structure5.36e-1526
reproductive system5.36e-1526
reproductive organ6.47e-1424
renal system8.21e-1319
urinary system structure1.26e-1218
kidney3.64e-1114
kidney mesenchyme3.64e-1114
upper urinary tract3.64e-1114
kidney rudiment3.64e-1114
kidney field3.64e-1114
gonad7.90e-1118
gonad primordium7.90e-1118
external genitalia3.13e-1017
indifferent external genitalia3.13e-1017
indifferent gonad3.13e-1017
male organism4.27e-0916
male reproductive system4.27e-0916
male reproductive organ7.79e-0915
intermediate mesoderm1.84e-0814
testis4.68e-0814


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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