MCL coexpression mm9:2686

Phase1 CAGE Peaks

	Short description
Mm9::chr11:57997297..57997319,+	p2@Gm12250
Mm9::chr11:57997328..57997373,+	p1@Gm12250
Mm9::chr5:65324789..65324845,-	p1@Tlr1

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:0032493	response to bacterial lipoprotein	0.00103179386036998
GO:0042495	detection of triacylated bacterial lipoprotein	0.00103179386036998
GO:0045335	phagocytic vesicle	0.00103179386036998
GO:0032490	detection of molecule of bacterial origin	0.00103179386036998
GO:0042497	triacylated lipoprotein binding	0.00103179386036998
GO:0042494	detection of bacterial lipoprotein	0.00103179386036998
GO:0016045	detection of bacterium	0.00265318421237996
GO:0042535	positive regulation of tumor necrosis factor biosynthetic process	0.00285727530563996
GO:0009595	detection of biotic stimulus	0.00285727530563996
GO:0007250	activation of NF-kappaB-inducing kinase	0.00285727530563996
GO:0042533	tumor necrosis factor biosynthetic process	0.00285727530563996
GO:0042534	regulation of tumor necrosis factor biosynthetic process	0.00285727530563996
GO:0045410	positive regulation of interleukin-6 biosynthetic process	0.00285727530563996
GO:0042116	macrophage activation	0.00353757894983995
GO:0045408	regulation of interleukin-6 biosynthetic process	0.00371445789733195
GO:0042226	interleukin-6 biosynthetic process	0.00386922697638745
GO:0030139	endocytic vesicle	0.00447110672826993
GO:0008034	lipoprotein binding	0.00447110672826993
GO:0032640	tumor necrosis factor production	0.00488744460175256
GO:0032635	interleukin-6 production	0.00495261052977593
GO:0002237	response to molecule of bacterial origin	0.00501157017893993
GO:0009593	detection of chemical stimulus	0.00590936483666446
GO:0002274	myeloid leukocyte activation	0.00726741762521468
GO:0032147	activation of protein kinase activity	0.00773845395277489
GO:0042108	positive regulation of cytokine biosynthetic process	0.00792417684764149
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.00833371964144987
GO:0045727	positive regulation of translation	0.00917150098106653
GO:0031328	positive regulation of cellular biosynthetic process	0.00950724342769486
GO:0009581	detection of external stimulus	0.010246780406433
GO:0042035	regulation of cytokine biosynthetic process	0.0103179386036999
GO:0009891	positive regulation of biosynthetic process	0.0105842079870211
GO:0042089	cytokine biosynthetic process	0.0114435319059217
GO:0042107	cytokine metabolic process	0.0114435319059217
GO:0051606	detection of stimulus	0.0125584052719318
GO:0051247	positive regulation of protein metabolic process	0.0125584052719318
GO:0045860	positive regulation of protein kinase activity	0.0141276390112198
GO:0033674	positive regulation of kinase activity	0.0141276390112198
GO:0051347	positive regulation of transferase activity	0.0141276390112198
GO:0045087	innate immune response	0.0141276390112198
GO:0001816	cytokine production	0.0153221388264943
GO:0009617	response to bacterium	0.0169113530285032
GO:0045859	regulation of protein kinase activity	0.0181685440630367
GO:0006417	regulation of translation	0.0181685440630367
GO:0043549	regulation of kinase activity	0.0181685440630367
GO:0043085	positive regulation of catalytic activity	0.0181685440630367
GO:0051338	regulation of transferase activity	0.0181685440630367
GO:0031326	regulation of cellular biosynthetic process	0.0183088527563525
GO:0009889	regulation of biosynthetic process	0.0199910060446685
GO:0051707	response to other organism	0.020720105277634
GO:0016023	cytoplasmic membrane-bound vesicle	0.0231534542267025
GO:0031988	membrane-bound vesicle	0.0235491775190326
GO:0045321	leukocyte activation	0.0239605463130363
GO:0006954	inflammatory response	0.0239605463130363
GO:0009607	response to biotic stimulus	0.0239605463130363
GO:0007243	protein kinase cascade	0.0244314046223321
GO:0001775	cell activation	0.0244314046223321
GO:0051246	regulation of protein metabolic process	0.02486978994478
GO:0051704	multi-organism process	0.02486978994478
GO:0050790	regulation of catalytic activity	0.0280158265137749
GO:0009611	response to wounding	0.0294314970007176
GO:0031410	cytoplasmic vesicle	0.0294314970007176
GO:0031982	vesicle	0.0296557525674083
GO:0065009	regulation of a molecular function	0.0304624854013996
GO:0031325	positive regulation of cellular metabolic process	0.0337590053689804
GO:0009893	positive regulation of metabolic process	0.0350492437491835
GO:0042221	response to chemical stimulus	0.0393621657776968
GO:0006412	translation	0.0393621657776968
GO:0009605	response to external stimulus	0.0398757980154753
GO:0006955	immune response	0.042797014904042

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
endoderm-derived structure	2.02e-15	118
endoderm	2.02e-15	118
presumptive endoderm	2.02e-15	118
digestive system	3.74e-15	116
digestive tract	3.74e-15	116
primitive gut	3.74e-15	116
subdivision of digestive tract	1.29e-14	114
hemolymphoid system	2.74e-13	48
immune system	2.74e-13	48
hematopoietic system	3.37e-12	45
blood island	3.37e-12	45
gastrointestinal system	9.28e-10	47
intestine	3.94e-08	31
gut epithelium	4.89e-08	55
mixed endoderm/mesoderm-derived structure	5.43e-08	35
unilaminar epithelium	2.06e-07	66
hemopoietic organ	2.09e-07	29
immune organ	2.09e-07	29
endo-epithelium	2.21e-07	69
foregut	8.10e-07	80

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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