MCL coexpression mm9:991

Phase1 CAGE Peaks

	Short description
Mm9::chr2:74535720..74535731,+	p6@Hoxd9
Mm9::chr2:74535796..74535808,+	p3@Hoxd9
Mm9::chr2:74536003..74536008,+	p7@Hoxd9
Mm9::chr2:74536026..74536039,+	p1@Hoxd9
Mm9::chr2:74536050..74536065,+	p2@Hoxd9
Mm9::chr2:74536071..74536083,+	p4@Hoxd9
Mm9::chr2:74547770..74547771,+	p@chr2:74547770..74547771 +
Mm9::chr2:74549968..74549996,+	p1@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

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GO ID	GO name	FDR corrected p-value
GO:0007389	pattern specification process	0.00833645111298099
GO:0005667	transcription factor complex	0.00833645111298099
GO:0043565	sequence-specific DNA binding	0.00833645111298099
GO:0009887	organ morphogenesis	0.00833645111298099
GO:0044451	nucleoplasm part	0.00833645111298099
GO:0005654	nucleoplasm	0.00833645111298099
GO:0030878	thyroid gland development	0.00876352118929734
GO:0031981	nuclear lumen	0.00883635242581507
GO:0031974	membrane-enclosed lumen	0.00899439116634181
GO:0043233	organelle lumen	0.00899439116634181
GO:0003700	transcription factor activity	0.00986557089874141
GO:0044428	nuclear part	0.0132477209712142
GO:0009653	anatomical structure morphogenesis	0.0158880744910698
GO:0048513	organ development	0.0196098476524455
GO:0035270	endocrine system development	0.0196098476524455
GO:0043234	protein complex	0.0239772212963834
GO:0048731	system development	0.0239772212963834
GO:0048732	gland development	0.0239772212963834
GO:0006355	regulation of transcription, DNA-dependent	0.0239772212963834
GO:0006351	transcription, DNA-dependent	0.0239772212963834
GO:0032774	RNA biosynthetic process	0.0239772212963834
GO:0003677	DNA binding	0.0239772212963834
GO:0045449	regulation of transcription	0.0239772212963834
GO:0048856	anatomical structure development	0.0239772212963834
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0239772212963834
GO:0006350	transcription	0.0239772212963834
GO:0032991	macromolecular complex	0.0239772212963834
GO:0010468	regulation of gene expression	0.0240249430055953
GO:0031323	regulation of cellular metabolic process	0.0251371079575476
GO:0007275	multicellular organismal development	0.0252864587535295
GO:0019222	regulation of metabolic process	0.0252864587535295
GO:0016070	RNA metabolic process	0.0258064807770019
GO:0044446	intracellular organelle part	0.0260279821068564
GO:0044422	organelle part	0.0260279821068564
GO:0016563	transcription activator activity	0.0310545188630561
GO:0010467	gene expression	0.032851226006689
GO:0003676	nucleic acid binding	0.0335243983959264
GO:0032502	developmental process	0.0347664881354756
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0369379254886281
GO:0050794	regulation of cellular process	0.0414194459809722

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
reproductive structure	8.52e-20	26
reproductive system	8.52e-20	26
reproductive organ	6.10e-19	24
cavitated compound organ	1.59e-18	21
gonad	3.38e-15	18
gonad primordium	3.38e-15	18
renal system	3.95e-15	19
urinary system structure	3.97e-15	18
external genitalia	2.32e-14	17
indifferent external genitalia	2.32e-14	17
indifferent gonad	2.32e-14	17
kidney	3.09e-13	14
kidney mesenchyme	3.09e-13	14
upper urinary tract	3.09e-13	14
kidney rudiment	3.09e-13	14
kidney field	3.09e-13	14
male organism	9.76e-13	16
male reproductive system	9.76e-13	16
male reproductive organ	1.02e-12	15
testis	7.23e-12	14
female organism	9.28e-09	11
intermediate mesoderm	4.67e-08	14
female reproductive system	1.94e-07	9
internal genitalia	2.52e-07	9
body cavity precursor	5.80e-07	38

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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