MCL coexpression mm9:1876

Phase1 CAGE Peaks

	Short description
Mm9::chr10:126778639..126778670,-	p3@Gli1
Mm9::chr10:126778916..126778974,-	p1@Gli1
Mm9::chr10:126779021..126779032,-	p2@Gli1
Mm9::chr13:63674708..63674738,-	p1@Ptch1

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:0007224	smoothened signaling pathway	0.000383498602969375
GO:0009953	dorsal/ventral pattern formation	0.000458067775768976
GO:0048732	gland development	0.000913430094021413
GO:0003002	regionalization	0.00272177480718542
GO:0043109	regulation of smoothened activity	0.00291319800441589
GO:0048598	embryonic morphogenesis	0.00291319800441589
GO:0035295	tube development	0.00291319800441589
GO:0007389	pattern specification process	0.00336672667248463
GO:0007418	ventral midline development	0.00336672667248463
GO:0005113	patched binding	0.00336672667248463
GO:0060032	notochord regression	0.00336672667248463
GO:0060033	anatomical structure regression	0.00462912235634527
GO:0048570	notochord morphogenesis	0.00529028061488478
GO:0021938	smoothened signaling pathway in regulation of granule cell precursor cell proliferation	0.00529028061488478
GO:0009790	embryonic development	0.0067420677676526
GO:0021937	Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation	0.00685664389347801
GO:0009887	organ morphogenesis	0.00685664389347801
GO:0030903	notochord development	0.00685664389347801
GO:0015485	cholesterol binding	0.00685664389347801
GO:0008158	hedgehog receptor activity	0.00685664389347801
GO:0040015	negative regulation of multicellular organism growth	0.00685664389347801
GO:0021940	positive regulation of granule cell precursor proliferation	0.00685664389347801
GO:0021936	regulation of granule cell precursor proliferation	0.00685664389347801
GO:0021534	cell proliferation in hindbrain	0.00685664389347801
GO:0009954	proximal/distal pattern formation	0.00685664389347801
GO:0021924	cell proliferation in the external granule layer	0.00685664389347801
GO:0021930	granule cell precursor proliferation	0.00685664389347801
GO:0007399	nervous system development	0.00690808382009827
GO:0008589	regulation of smoothened signaling pathway	0.00766010646861597
GO:0032934	sterol binding	0.00835976554417887
GO:0021696	cerebellar cortex morphogenesis	0.00835976554417887
GO:0021587	cerebellum morphogenesis	0.0086767510059229
GO:0021575	hindbrain morphogenesis	0.00897449448372583
GO:0021695	cerebellar cortex development	0.00951885273914528
GO:0021983	pituitary gland development	0.00951885273914528
GO:0021536	diencephalon development	0.010282147655304
GO:0048562	embryonic organ morphogenesis	0.0105041764495005
GO:0030879	mammary gland development	0.0106411477768241
GO:0022037	metencephalon development	0.0106411477768241
GO:0021549	cerebellum development	0.0106411477768241
GO:0045926	negative regulation of growth	0.0112837374470277
GO:0009653	anatomical structure morphogenesis	0.0148410287656804
GO:0048568	embryonic organ development	0.0159179525336601
GO:0030902	hindbrain development	0.0176559464142327
GO:0008017	microtubule binding	0.0184936621275853
GO:0005496	steroid binding	0.0184936621275853
GO:0048513	organ development	0.0184936621275853
GO:0035270	endocrine system development	0.0184936621275853
GO:0040014	regulation of multicellular organism growth	0.0195162687051387
GO:0001841	neural tube formation	0.0195162687051387
GO:0015631	tubulin binding	0.0195162687051387
GO:0001839	neural plate morphogenesis	0.0195162687051387
GO:0001840	neural plate development	0.0195162687051387
GO:0001838	embryonic epithelial tube formation	0.0195162687051387
GO:0008201	heparin binding	0.0196770816090132
GO:0035264	multicellular organism growth	0.0196770816090132
GO:0030326	embryonic limb morphogenesis	0.0196770816090132
GO:0035113	embryonic appendage morphogenesis	0.0196770816090132
GO:0030324	lung development	0.0196770816090132
GO:0030323	respiratory tube development	0.0196770816090132
GO:0021915	neural tube development	0.0196770816090132
GO:0016485	protein processing	0.0196770816090132
GO:0016331	morphogenesis of embryonic epithelium	0.0209617737932445
GO:0048731	system development	0.0209617737932445
GO:0005539	glycosaminoglycan binding	0.0209617737932445
GO:0035107	appendage morphogenesis	0.0209617737932445
GO:0035108	limb morphogenesis	0.0209617737932445
GO:0060173	limb development	0.02115589848994
GO:0048736	appendage development	0.02115589848994
GO:0030247	polysaccharide binding	0.0213804384406477
GO:0001871	pattern binding	0.0221178296671192
GO:0008270	zinc ion binding	0.0236848855557652
GO:0003682	chromatin binding	0.0246230452223987
GO:0048856	anatomical structure development	0.0246230452223987
GO:0030900	forebrain development	0.0246230452223987
GO:0002009	morphogenesis of an epithelium	0.0298689584953271
GO:0007275	multicellular organismal development	0.0299029695567251
GO:0046914	transition metal ion binding	0.0336744915261688
GO:0035239	tube morphogenesis	0.0341194293784279
GO:0040008	regulation of growth	0.0341194293784279
GO:0007166	cell surface receptor linked signal transduction	0.0378219578990228
GO:0008284	positive regulation of cell proliferation	0.0395196813844614
GO:0016563	transcription activator activity	0.0395196813844614
GO:0007420	brain development	0.0403588074381917
GO:0007283	spermatogenesis	0.0417053039818248
GO:0048232	male gamete generation	0.0417053039818248
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0417053039818248
GO:0032502	developmental process	0.0453064908291446
GO:0043009	chordate embryonic development	0.0457045477608513
GO:0009792	embryonic development ending in birth or egg hatching	0.0458064619401872
GO:0007417	central nervous system development	0.046709802065086
GO:0045893	positive regulation of transcription, DNA-dependent	0.0471956256633701
GO:0007276	gamete generation	0.0494386906563075

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
multi-cellular organism	5.76e-08	333

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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