MCL coexpression mm9:1732

Phase1 CAGE Peaks

	Short description
Mm9::chr19:55972403..55972421,+	p22@Tcf7l2
Mm9::chr19:55972431..55972440,+	p63@Tcf7l2
Mm9::chr19:55972441..55972456,+	p18@Tcf7l2
Mm9::chr19:55985049..55985067,+	p@chr19:55985049..55985067 +
Mm9::chr1:140743964..140743976,-	p3@Lhx9

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:0007548	sex differentiation	0.00119582923147353
GO:0003006	reproductive developmental process	0.00119582923147353
GO:0022414	reproductive process	0.00460555115778634
GO:0048619	embryonic hindgut morphogenesis	0.00597129392711993
GO:0030538	embryonic genitalia morphogenesis	0.00597129392711993
GO:0035112	genitalia morphogenesis	0.00597129392711993
GO:0005667	transcription factor complex	0.00651360345025033
GO:0000003	reproduction	0.00651360345025033
GO:0007442	hindgut morphogenesis	0.00651360345025033
GO:0048613	embryonic ectodermal gut morphogenesis	0.00651360345025033
GO:0048611	embryonic ectodermal gut development	0.00651360345025033
GO:0044451	nucleoplasm part	0.00674830909527291
GO:0048558	embryonic gut morphogenesis	0.00674830909527291
GO:0005654	nucleoplasm	0.00674830909527291
GO:0048557	embryonic digestive tract morphogenesis	0.00674830909527291
GO:0007439	ectodermal gut development	0.00674830909527291
GO:0048567	ectodermal gut morphogenesis	0.00674830909527291
GO:0048547	gut morphogenesis	0.00674830909527291
GO:0048806	genitalia development	0.00674830909527291
GO:0031981	nuclear lumen	0.00674830909527291
GO:0048566	embryonic gut development	0.00674830909527291
GO:0048546	digestive tract morphogenesis	0.00674830909527291
GO:0008013	beta-catenin binding	0.00674830909527291
GO:0031974	membrane-enclosed lumen	0.00700277597950898
GO:0043233	organelle lumen	0.00700277597950898
GO:0008584	male gonad development	0.00767422299235825
GO:0003700	transcription factor activity	0.00767422299235825
GO:0048565	gut development	0.00767422299235825
GO:0048562	embryonic organ morphogenesis	0.00864381628664263
GO:0046546	development of primary male sexual characteristics	0.00915096731892564
GO:0044428	nuclear part	0.00998157778245865
GO:0046661	male sex differentiation	0.0100699331827434
GO:0008585	female gonad development	0.0122628934130942
GO:0046545	development of primary female sexual characteristics	0.0122628934130942
GO:0046660	female sex differentiation	0.0122628934130942
GO:0048568	embryonic organ development	0.0122628934130942
GO:0048513	organ development	0.0154657633070033
GO:0008406	gonad development	0.0160071329758149
GO:0048608	reproductive structure development	0.0162074394662785
GO:0045137	development of primary sexual characteristics	0.0172906600818872
GO:0021915	neural tube development	0.0188968127462959
GO:0043234	protein complex	0.0188968127462959
GO:0048731	system development	0.0202777454796801
GO:0006355	regulation of transcription, DNA-dependent	0.0236243024285655
GO:0006351	transcription, DNA-dependent	0.0236243024285655
GO:0032774	RNA biosynthetic process	0.0236243024285655
GO:0003677	DNA binding	0.0237089321221221
GO:0045449	regulation of transcription	0.0238839324386906
GO:0048856	anatomical structure development	0.0238839324386906
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0238839324386906
GO:0006350	transcription	0.024032443516949
GO:0032991	macromolecular complex	0.0242324733088106
GO:0010468	regulation of gene expression	0.0247048942227348
GO:0031323	regulation of cellular metabolic process	0.0261887583221484
GO:0016055	Wnt receptor signaling pathway	0.0261887583221484
GO:0007275	multicellular organismal development	0.0265189796586637
GO:0019222	regulation of metabolic process	0.0267678396391529
GO:0016070	RNA metabolic process	0.0277133635930366
GO:0044446	intracellular organelle part	0.0287082445500029
GO:0044422	organelle part	0.0287082445500029
GO:0010467	gene expression	0.0377243021012196
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0377243021012196
GO:0048598	embryonic morphogenesis	0.0377243021012196
GO:0003676	nucleic acid binding	0.0377243021012196
GO:0032502	developmental process	0.0395612071036099
GO:0043009	chordate embryonic development	0.0396857185934148
GO:0009792	embryonic development ending in birth or egg hatching	0.0396857185934148
GO:0045893	positive regulation of transcription, DNA-dependent	0.0406374537402066
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0406374537402066
GO:0050794	regulation of cellular process	0.0460685674686323
GO:0045941	positive regulation of transcription	0.0469057581963048
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0472341004380639

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
CNS neuron (sensu Vertebrata)	2.05e-10	23
neuroblast (sensu Vertebrata)	2.05e-10	23
striatum neuron	2.52e-08	3
granule cell	5.27e-08	3
raphe nuclei neuron	5.27e-08	3

Uber Anatomy

Ontology term	p-value	n
basal ganglion	4.51e-10	8
nuclear complex of neuraxis	4.51e-10	8
aggregate regional part of brain	4.51e-10	8
collection of basal ganglia	4.51e-10	8
cerebral subcortex	4.51e-10	8
corpus striatum	3.51e-08	5
striatum	3.51e-08	5
ventral part of telencephalon	3.51e-08	5
future corpus striatum	3.51e-08	5
raphe nuclei	5.27e-08	3
reticular formation	5.27e-08	3

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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