MCL coexpression mm9:973

Phase1 CAGE Peaks

	Short description
Mm9::chr18:34784216..34784245,-	p1@Brd8
Mm9::chr1:15795720..15795756,+	p1@Terf1
Mm9::chr1:180267871..180267892,-	p3@Hnrnpu
Mm9::chr3:95021663..95021687,-	p3@Gabpb2
Mm9::chr4:32702403..32702443,+	p1@Casp8ap2
Mm9::chr5:144670842..144670916,+	p1@Pms2
Mm9::chr8:108160409..108160489,+	p1@Ctcf
Mm9::chr9:15162136..15162203,-	p1@5830418K08Rik

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:0006259	DNA metabolic process	0.00669822721368301
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00770354454023687
GO:0045449	regulation of transcription	0.00770354454023687
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00770354454023687
GO:0006350	transcription	0.00770354454023687
GO:0010468	regulation of gene expression	0.00770354454023687
GO:0031323	regulation of cellular metabolic process	0.00800692130460139
GO:0019222	regulation of metabolic process	0.00833682578190896
GO:0005634	nucleus	0.01069598650413
GO:0043283	biopolymer metabolic process	0.0107983267282468
GO:0032389	MutLalpha complex	0.0107983267282468
GO:0022402	cell cycle process	0.0107983267282468
GO:0010467	gene expression	0.0107983267282468
GO:0006260	DNA replication	0.0107983267282468
GO:0043028	caspase regulator activity	0.0107983267282468
GO:0010216	maintenance of DNA methylation	0.0107983267282468
GO:0042162	telomeric DNA binding	0.0107983267282468
GO:0008656	caspase activator activity	0.0107983267282468
GO:0007004	telomere maintenance via telomerase	0.0129558623042775
GO:0032300	mismatch repair complex	0.0129558623042775
GO:0007049	cell cycle	0.0138056554840343
GO:0042802	identical protein binding	0.0138056554840343
GO:0006278	RNA-dependent DNA replication	0.014765556762504
GO:0008625	induction of apoptosis via death domain receptors	0.014765556762504
GO:0016505	apoptotic protease activator activity	0.014765556762504
GO:0050794	regulation of cellular process	0.014765556762504
GO:0006355	regulation of transcription, DNA-dependent	0.014765556762504
GO:0006349	genetic imprinting	0.014765556762504
GO:0009048	dosage compensation, by inactivation of X chromosome	0.014765556762504
GO:0006351	transcription, DNA-dependent	0.014765556762504
GO:0032774	RNA biosynthetic process	0.014765556762504
GO:0003677	DNA binding	0.0149914116052312
GO:0002566	somatic diversification of immune receptors via somatic mutation	0.0151983381739104
GO:0016446	somatic hypermutation of immunoglobulin genes	0.0151983381739104
GO:0000279	M phase	0.0151983381739104
GO:0043170	macromolecule metabolic process	0.0151983381739104
GO:0030983	mismatched DNA binding	0.015329864948429
GO:0007549	dosage compensation	0.015329864948429
GO:0050789	regulation of biological process	0.0165727056289125
GO:0006298	mismatch repair	0.0176438701986368
GO:0022403	cell cycle phase	0.0176438701986368
GO:0044424	intracellular part	0.0176438701986368
GO:0016504	protease activator activity	0.0176438701986368
GO:0045005	maintenance of fidelity during DNA-dependent DNA replication	0.0176438701986368
GO:0016070	RNA metabolic process	0.020206969527929
GO:0005622	intracellular	0.020206969527929
GO:0006305	DNA alkylation	0.020206969527929
GO:0006306	DNA methylation	0.020206969527929
GO:0065007	biological regulation	0.0206084635137446
GO:0032200	telomere organization and biogenesis	0.0215470177903846
GO:0000723	telomere maintenance	0.0215470177903846
GO:0000781	chromosome, telomeric region	0.0219499579438009
GO:0006304	DNA modification	0.0219499579438009
GO:0044238	primary metabolic process	0.0220368393534729
GO:0008624	induction of apoptosis by extracellular signals	0.0220368393534729
GO:0044237	cellular metabolic process	0.0220368393534729
GO:0006919	caspase activation	0.0220368393534729
GO:0043231	intracellular membrane-bound organelle	0.0220368393534729
GO:0043227	membrane-bound organelle	0.0220368393534729
GO:0003690	double-stranded DNA binding	0.0222388548665342
GO:0043280	positive regulation of caspase activity	0.0222388548665342
GO:0051276	chromosome organization and biogenesis	0.0228546865612764
GO:0051345	positive regulation of hydrolase activity	0.0245968543146773
GO:0016445	somatic diversification of immunoglobulins	0.030235839008093
GO:0003676	nucleic acid binding	0.0302919443924271
GO:0043281	regulation of caspase activity	0.0302919443924271
GO:0002200	somatic diversification of immune receptors	0.0307973407813843
GO:0002377	immunoglobulin production	0.0364478222951602
GO:0002440	production of molecular mediator of immune response	0.0364478222951602
GO:0043229	intracellular organelle	0.0364478222951602
GO:0043226	organelle	0.0364478222951602
GO:0043414	biopolymer methylation	0.037552721260962
GO:0040029	regulation of gene expression, epigenetic	0.0379139366498252
GO:0032259	methylation	0.0391283390029987
GO:0006261	DNA-dependent DNA replication	0.0394580715189841
GO:0043566	structure-specific DNA binding	0.0406185367480307
GO:0008632	apoptotic program	0.0409195318913317

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
hemopoietic organ	4.00e-12	29
immune organ	4.00e-12	29
anterior region of body	4.64e-10	43
thymus	5.72e-09	23
neck	5.72e-09	23
respiratory system epithelium	5.72e-09	23
hemolymphoid system gland	5.72e-09	23
pharyngeal epithelium	5.72e-09	23
thymic region	5.72e-09	23
pharyngeal gland	5.72e-09	23
entire pharyngeal arch endoderm	5.72e-09	23
thymus primordium	5.72e-09	23
early pharyngeal endoderm	5.72e-09	23
mixed endoderm/mesoderm-derived structure	5.80e-09	35
primordium	7.74e-09	134
gland of gut	2.53e-08	24
pharynx	4.27e-08	24
upper respiratory tract	4.27e-08	24
chordate pharynx	4.27e-08	24
pharyngeal arch system	4.27e-08	24
pharyngeal region of foregut	4.27e-08	24
hematopoietic system	4.54e-08	45
blood island	4.54e-08	45
craniocervical region	4.62e-08	36
respiratory tract	1.72e-07	41
hemolymphoid system	2.21e-07	48
immune system	2.21e-07	48
respiratory system	4.09e-07	42

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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