MCL coexpression mm9:781

Phase1 CAGE Peaks

	Short description
Mm9::chr11:21501144..21501147,+	p@chr11:21501144..21501147 +
Mm9::chr11:48715513..48715546,-	p@chr11:48715513..48715546 -
Mm9::chr11:6129264..6129275,-	p@chr11:6129264..6129275 -
Mm9::chr11:9019226..9019233,+	p@chr11:9019226..9019233 +
Mm9::chr11:9019282..9019299,+	p@chr11:9019282..9019299 +
Mm9::chr15:77490274..77490279,-	p@chr15:77490274..77490279 -
Mm9::chr18:73975357..73975368,-	p3@Me2
Mm9::chr19:53102858..53102869,-	p@chr19:53102858..53102869 -
Mm9::chr9:31720903..31720918,-	p2@Barx2

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:0000122	negative regulation of transcription from RNA polymerase II promoter	0.00365576547784741
GO:0045892	negative regulation of transcription, DNA-dependent	0.00365576547784741
GO:0016481	negative regulation of transcription	0.00365576547784741
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00365576547784741
GO:0042637	catagen	0.00365576547784741
GO:0031324	negative regulation of cellular metabolic process	0.00365576547784741
GO:0009892	negative regulation of metabolic process	0.00400373694120981
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.00456441499641985
GO:0005667	transcription factor complex	0.00456441499641985
GO:0006366	transcription from RNA polymerase II promoter	0.00456441499641985
GO:0044451	nucleoplasm part	0.00635773056744951
GO:0005654	nucleoplasm	0.00640120353318183
GO:0031981	nuclear lumen	0.00835083855626479
GO:0048820	hair follicle maturation	0.00863300937840844
GO:0031974	membrane-enclosed lumen	0.00863300937840844
GO:0043233	organelle lumen	0.00863300937840844
GO:0048523	negative regulation of cellular process	0.0101479934017225
GO:0048519	negative regulation of biological process	0.011067884623619
GO:0044428	nuclear part	0.0128492932728319
GO:0045445	myoblast differentiation	0.0161890987055238
GO:0022404	molting cycle process	0.0161890987055238
GO:0001942	hair follicle development	0.0161890987055238
GO:0022405	hair cycle process	0.0161890987055238
GO:0042633	hair cycle	0.0161890987055238
GO:0042303	molting cycle	0.0161890987055238
GO:0003714	transcription corepressor activity	0.0202653465137349
GO:0042692	muscle cell differentiation	0.0207599354898422
GO:0048741	skeletal muscle fiber development	0.0207599354898422
GO:0048747	muscle fiber development	0.0207599354898422
GO:0043234	protein complex	0.020873176648202
GO:0006355	regulation of transcription, DNA-dependent	0.0230245297652552
GO:0006351	transcription, DNA-dependent	0.0230245297652552
GO:0021700	developmental maturation	0.0230245297652552
GO:0032774	RNA biosynthetic process	0.0230245297652552
GO:0003677	DNA binding	0.0230245297652552
GO:0007519	skeletal muscle development	0.0230245297652552
GO:0008544	epidermis development	0.0230245297652552
GO:0045449	regulation of transcription	0.0230245297652552
GO:0003682	chromatin binding	0.0230245297652552
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0230245297652552
GO:0007398	ectoderm development	0.0230245297652552
GO:0006350	transcription	0.0230245297652552
GO:0032991	macromolecular complex	0.0231208919643697
GO:0010468	regulation of gene expression	0.0234789215736499
GO:0031323	regulation of cellular metabolic process	0.0248777568436999
GO:0014706	striated muscle development	0.0249088824294402
GO:0007275	multicellular organismal development	0.0249298079320954
GO:0019222	regulation of metabolic process	0.0250795011298027
GO:0016070	RNA metabolic process	0.0255360665361971
GO:0003712	transcription cofactor activity	0.0255360665361971
GO:0044446	intracellular organelle part	0.0261352402748791
GO:0044422	organelle part	0.0261352402748791
GO:0016564	transcription repressor activity	0.027089289112185
GO:0007517	muscle development	0.0288363997579811
GO:0008134	transcription factor binding	0.031875321855894
GO:0010467	gene expression	0.0324322052668077
GO:0003676	nucleic acid binding	0.0334193720851622
GO:0032502	developmental process	0.0349805674959158
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.037496913465151
GO:0050794	regulation of cellular process	0.0424056232662334
GO:0009888	tissue development	0.0430751330345371

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>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
brush border epithelial cell	1.52e-20	6
gut absorptive cell	1.52e-20	6
absorptive cell	1.52e-20	6
enterocyte	1.52e-20	6
intestinal epithelial cell	6.35e-18	9
epithelial cell of alimentary canal	6.35e-18	9
columnar/cuboidal epithelial cell	1.55e-17	7
epithelial cell	3.30e-12	25
transporting cell	2.57e-11	3
M cell of gut	2.57e-11	3
endo-epithelial cell	2.04e-10	15
endodermal cell	1.35e-07	20

Uber Anatomy

Ontology term	p-value	n
intestine	2.04e-37	31
mucosa	5.17e-37	15
intestinal mucosa	6.08e-31	13
anatomical wall	6.08e-31	13
wall of intestine	6.08e-31	13
gastrointestinal system mucosa	6.08e-31	13
gastrointestinal system	1.84e-23	47
organ component layer	3.24e-22	24
epithelium of mucosa	6.35e-18	9
gastrointestinal system epithelium	6.35e-18	9
intestinal epithelium	6.35e-18	9
small intestine	9.58e-15	4
simple columnar epithelium	1.63e-14	11
ileal mucosa	1.06e-11	3
ileum	1.06e-11	3
mucosa of small intestine	1.06e-11	3
wall of small intestine	1.06e-11	3
digestive system	1.99e-09	116
digestive tract	1.99e-09	116
primitive gut	1.99e-09	116
endoderm-derived structure	3.37e-09	118
endoderm	3.37e-09	118
presumptive endoderm	3.37e-09	118
gut-associated lymphoid tissue	1.31e-07	2
mucosa-associated lymphoid tissue	1.31e-07	2
lymphoid tissue	1.31e-07	2
subdivision of digestive tract	1.66e-07	114

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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