MCL coexpression mm9:391

Phase1 CAGE Peaks

	Short description
Mm9::chr10:60881031..60881037,+	p1@Nodal
Mm9::chr12:106460922..106460932,-	p1@Tcl1
Mm9::chr12:106460944..106460955,-	p2@Tcl1
Mm9::chr16:48281766..48281778,+	p@chr16:48281766..48281778 +
Mm9::chr17:35642973..35642994,+	p2@Pou5f1
Mm9::chr17:35642997..35643014,+	p1@Pou5f1
Mm9::chr1:182823238..182823239,+	p1@Lefty2
Mm9::chr1:182865168..182865172,+	p2@Lefty1
Mm9::chr2:118541186..118541194,-	p@chr2:118541186..118541194 -
Mm9::chr2:165635739..165635747,+	p@chr2:165635739..165635747 +
Mm9::chr2:25621051..25621055,+	p1@Lcn3
Mm9::chr6:122576436..122576438,+	p1@Dppa3
Mm9::chr6:122657610..122657626,+	p1@Nanog p1@Nanogpd
Mm9::chr7:19572867..19572873,+	p1@Nanos2
Mm9::chr7:88599637..88599650,-	p4@Cpeb1
Mm9::chr9:78215959..78215971,-	p1@Dppa5a
Mm9::chr9:78215974..78215984,-	p2@Dppa5a
Mm9::chr9:78215998..78216003,-	p3@Dppa5a
Mm9::chrX:140770330..140770374,+	p5@Alg13

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:0048863	stem cell differentiation	2.7667001875512e-06
GO:0048864	stem cell development	0.000451023744568524
GO:0019827	stem cell maintenance	0.000451023744568524
GO:0042074	cell migration involved in gastrulation	0.000630972040384902
GO:0045596	negative regulation of cell differentiation	0.000948523766910004
GO:0045120	pronucleus	0.00124038586237459
GO:0051093	negative regulation of developmental process	0.00124038586237459
GO:0008083	growth factor activity	0.00304482699284934
GO:0045595	regulation of cell differentiation	0.00304482699284934
GO:0009790	embryonic development	0.00342597435615527
GO:0005125	cytokine activity	0.00670187390332782
GO:0007389	pattern specification process	0.00788911411822714
GO:0050793	regulation of developmental process	0.00788911411822714
GO:0001714	endodermal cell fate specification	0.00788911411822714
GO:0042664	negative regulation of endodermal cell fate specification	0.00788911411822714
GO:0002085	repression of premature neural plate formation	0.00788911411822714
GO:0030718	germ-line stem cell maintenance	0.00788911411822714
GO:0042663	regulation of endodermal cell fate specification	0.00788911411822714
GO:0004577	N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity	0.00788911411822714
GO:0007369	gastrulation	0.00835616358503614
GO:0032502	developmental process	0.00842780921854488
GO:0032501	multicellular organismal process	0.0105943426963285
GO:0007275	multicellular organismal development	0.010703428565192
GO:0001711	endodermal cell fate commitment	0.010703428565192
GO:0042659	regulation of cell fate specification	0.010703428565192
GO:0010453	regulation of cell fate commitment	0.010703428565192
GO:0009996	negative regulation of cell fate specification	0.010703428565192
GO:0010454	negative regulation of cell fate commitment	0.010703428565192
GO:0048523	negative regulation of cellular process	0.0116737389182239
GO:0009952	anterior/posterior pattern formation	0.012727101419578
GO:0045165	cell fate commitment	0.0138066231261762
GO:0048519	negative regulation of biological process	0.0138066231261762
GO:0030259	lipid glycosylation	0.0176185544395488
GO:0001940	male pronucleus	0.0176185544395488
GO:0006417	regulation of translation	0.0196990255106665
GO:0048505	regulation of timing of cell differentiation	0.0196990255106665
GO:0040034	regulation of development, heterochronic	0.0196990255106665
GO:0001939	female pronucleus	0.0196990255106665
GO:0031326	regulation of cellular biosynthetic process	0.0211316487213253
GO:0005160	transforming growth factor beta receptor binding	0.0218905462024405
GO:0040016	embryonic cleavage	0.0218905462024405
GO:0003002	regionalization	0.0218905462024405
GO:0009889	regulation of biosynthetic process	0.0237110789038901
GO:0007130	synaptonemal complex assembly	0.0238035645283384
GO:0065007	biological regulation	0.0271473139901545
GO:0017145	stem cell division	0.0288307489318434
GO:0005102	receptor binding	0.0288307489318434
GO:0009948	anterior/posterior axis specification	0.0342471769361994
GO:0007129	synapsis	0.0365870750233847
GO:0001947	heart looping	0.0406109439809507
GO:0048168	regulation of neuronal synaptic plasticity	0.0406109439809507
GO:0050794	regulation of cellular process	0.0406109439809507
GO:0051246	regulation of protein metabolic process	0.0413016207316092
GO:0051301	cell division	0.0419009446029893
GO:0009798	axis specification	0.0461078486046946

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
gonad	3.01e-25	18
gonad primordium	3.01e-25	18
testis	1.18e-22	14
male reproductive organ	3.54e-21	15
male organism	6.98e-20	16
male reproductive system	6.98e-20	16
reproductive organ	4.99e-19	24
external genitalia	9.72e-19	17
indifferent external genitalia	9.72e-19	17
indifferent gonad	9.72e-19	17
reproductive structure	1.37e-17	26
reproductive system	1.37e-17	26
body cavity	1.93e-12	37
body cavity or lining	1.93e-12	37
body cavity precursor	4.04e-12	38
anatomical cavity	8.16e-12	39
anatomical space	3.90e-08	57

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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