MCL coexpression mm9:1244

Phase1 CAGE Peaks

	Short description
Mm9::chr10:5636678..5636725,-	p6@Esr1
Mm9::chr6:52190656..52190667,-	p7@Hoxa10
Mm9::chr6:52190668..52190682,-	p3@Hoxa10
Mm9::chr6:52195747..52195762,-	p3@Hoxa11
Mm9::chr6:52195763..52195792,-	p2@Hoxa11
Mm9::chr6:52195795..52195825,-	p1@Hoxa11

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

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GO ID	GO name	FDR corrected p-value
GO:0043565	sequence-specific DNA binding	0.00128041237870629
GO:0003700	transcription factor activity	0.00425779343150948
GO:0009653	anatomical structure morphogenesis	0.00745703692690638
GO:0045839	negative regulation of mitosis	0.00821737696392652
GO:0007389	pattern specification process	0.00916575112443743
GO:0006355	regulation of transcription, DNA-dependent	0.00916575112443743
GO:0006351	transcription, DNA-dependent	0.00916575112443743
GO:0032774	RNA biosynthetic process	0.00916575112443743
GO:0003677	DNA binding	0.00916575112443743
GO:0045449	regulation of transcription	0.00916575112443743
GO:0048856	anatomical structure development	0.00916575112443743
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00916575112443743
GO:0006350	transcription	0.00916575112443743
GO:0010468	regulation of gene expression	0.0093978923010452
GO:0031323	regulation of cellular metabolic process	0.00961506158071779
GO:0005667	transcription factor complex	0.00961506158071779
GO:0019222	regulation of metabolic process	0.0097359320341928
GO:0016070	RNA metabolic process	0.00994272197671441
GO:0001759	induction of an organ	0.00997226994819038
GO:0010092	specification of organ identity	0.00997226994819038
GO:0009887	organ morphogenesis	0.00997226994819038
GO:0045168	cell-cell signaling during cell fate commitment	0.00997226994819038
GO:0031128	induction	0.00997226994819038
GO:0044451	nucleoplasm part	0.00997226994819038
GO:0005654	nucleoplasm	0.0105053104482289
GO:0010467	gene expression	0.0117982004492543
GO:0003676	nucleic acid binding	0.0122037722687037
GO:0032502	developmental process	0.0127500285248328
GO:0031981	nuclear lumen	0.0127500285248328
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0137472389941103
GO:0007088	regulation of mitosis	0.0142119381120271
GO:0031974	membrane-enclosed lumen	0.0142119381120271
GO:0043233	organelle lumen	0.0142119381120271
GO:0050794	regulation of cellular process	0.0149611027976701
GO:0050789	regulation of biological process	0.0200777394008583
GO:0001656	metanephros development	0.0201764519006285
GO:0005496	steroid binding	0.0201764519006285
GO:0003707	steroid hormone receptor activity	0.0201764519006285
GO:0004879	ligand-dependent nuclear receptor activity	0.0201764519006285
GO:0044428	nuclear part	0.0205358236401176
GO:0065007	biological regulation	0.0229268067524417
GO:0005634	nucleus	0.0238045419967062
GO:0043283	biopolymer metabolic process	0.025483047988348
GO:0001822	kidney development	0.027160817266496
GO:0001655	urogenital system development	0.0287305713925266
GO:0048513	organ development	0.0325860332208126
GO:0016049	cell growth	0.0327041000229519
GO:0045165	cell fate commitment	0.0340555540588183
GO:0008361	regulation of cell size	0.0352516481138001
GO:0005515	protein binding	0.0352516481138001
GO:0045786	negative regulation of progression through cell cycle	0.0371480088490407
GO:0043234	protein complex	0.03962013826808
GO:0048731	system development	0.0425824276148522
GO:0003002	regionalization	0.0443845586634856
GO:0043170	macromolecule metabolic process	0.0451761693242856
GO:0007067	mitosis	0.0482831052960478
GO:0000087	M phase of mitotic cell cycle	0.0482831052960478
GO:0000074	regulation of progression through cell cycle	0.0496525167121281
GO:0001501	skeletal development	0.0496525167121281

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

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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>

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Uber Anatomy

Ontology term	p-value	n
renal system	7.78e-16	19
urinary system structure	6.56e-15	18
cavitated compound organ	1.61e-14	21
kidney	3.54e-11	14
kidney mesenchyme	3.54e-11	14
upper urinary tract	3.54e-11	14
kidney rudiment	3.54e-11	14
kidney field	3.54e-11	14
female reproductive system	2.16e-10	9
female reproductive organ	2.41e-09	8
reproductive structure	2.85e-08	26
reproductive system	2.85e-08	26
surface structure	4.60e-08	22
forelimb	5.92e-08	7
pectoral appendage	5.92e-08	7
pectoral appendage bud	5.92e-08	7
forelimb bud	5.92e-08	7
forelimb/pectoral fin field	5.92e-08	7
female organism	6.63e-08	11
internal genitalia	1.94e-07	9
reproductive organ	8.13e-07	24

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

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
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