MCL coexpression mm9:3505

Phase1 CAGE Peaks

	Short description
Mm9::chr5:135028251..135028283,-	p4@Clip2
Mm9::chr5:135028284..135028314,-	p2@Clip2
Mm9::chr9:119311199..119311271,+	p1@Acvr2b

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:0048617	embryonic foregut morphogenesis	0.011145798098101
GO:0007440	foregut morphogenesis	0.011145798098101
GO:0060021	palate development	0.011145798098101
GO:0048613	embryonic ectodermal gut morphogenesis	0.011145798098101
GO:0005881	cytoplasmic microtubule	0.011145798098101
GO:0048611	embryonic ectodermal gut development	0.011145798098101
GO:0048185	activin binding	0.011145798098101
GO:0004712	protein serine/threonine/tyrosine kinase activity	0.011145798098101
GO:0048558	embryonic gut morphogenesis	0.011145798098101
GO:0048557	embryonic digestive tract morphogenesis	0.011145798098101
GO:0007439	ectodermal gut development	0.011145798098101
GO:0048567	ectodermal gut morphogenesis	0.011145798098101
GO:0006367	transcription initiation from RNA polymerase II promoter	0.011145798098101
GO:0048547	gut morphogenesis	0.011145798098101
GO:0004675	transmembrane receptor protein serine/threonine kinase activity	0.011145798098101
GO:0005024	transforming growth factor beta receptor activity	0.011145798098101
GO:0048546	digestive tract morphogenesis	0.0117080755149383
GO:0048566	embryonic gut development	0.0117080755149383
GO:0048565	gut development	0.0153558571126666
GO:0048562	embryonic organ morphogenesis	0.0170180089459955
GO:0048705	skeletal morphogenesis	0.0177502380498165
GO:0006352	transcription initiation	0.0184157393298989
GO:0001702	gastrulation with mouth forming second	0.0212276851367173
GO:0007368	determination of left/right symmetry	0.0212276851367173
GO:0009799	determination of symmetry	0.0212276851367173
GO:0009855	determination of bilateral symmetry	0.0212276851367173
GO:0042475	odontogenesis of dentine-containing teeth	0.0212276851367173
GO:0048568	embryonic organ development	0.0212276851367173
GO:0042476	odontogenesis	0.0212276851367173
GO:0004702	receptor signaling protein serine/threonine kinase activity	0.0247988829518103
GO:0019838	growth factor binding	0.0247988829518103
GO:0007498	mesoderm development	0.0247988829518103
GO:0007369	gastrulation	0.0304164743280477
GO:0001822	kidney development	0.0336412387697396
GO:0019199	transmembrane receptor protein kinase activity	0.0336412387697396
GO:0003702	RNA polymerase II transcription factor activity	0.0336412387697396
GO:0001655	urogenital system development	0.0336412387697396
GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	0.0336412387697396
GO:0005057	receptor signaling protein activity	0.0356762223841759
GO:0009952	anterior/posterior pattern formation	0.0380117155275296
GO:0065004	protein-DNA complex assembly	0.0473082376810146
GO:0030145	manganese ion binding	0.0496332098555546

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
neuron	1.50e-16	33
neuronal stem cell	1.50e-16	33
neuroblast	1.50e-16	33
electrically signaling cell	1.50e-16	33
CNS neuron (sensu Vertebrata)	2.61e-14	23
neuroblast (sensu Vertebrata)	2.61e-14	23
neural cell	3.61e-12	43
ectodermal cell	4.92e-12	44
neurectodermal cell	4.92e-12	44
electrically responsive cell	1.11e-11	39
electrically active cell	1.11e-11	39
non-terminally differentiated cell	7.18e-09	49

Uber Anatomy

Ontology term	p-value	n
nervous system	5.01e-21	75
central nervous system	2.97e-20	73
neurectoderm	7.53e-18	64
neural plate	7.53e-18	64
presumptive neural plate	7.53e-18	64
ectoderm-derived structure	1.30e-16	95
ectoderm	1.30e-16	95
presumptive ectoderm	1.30e-16	95
regional part of nervous system	3.77e-15	54
neural tube	3.37e-14	52
neural rod	3.37e-14	52
future spinal cord	3.37e-14	52
neural keel	3.37e-14	52
pre-chordal neural plate	6.25e-14	49
gray matter	3.29e-12	34
ecto-epithelium	4.29e-12	73
brain	6.18e-12	47
future brain	6.18e-12	47
anterior neural tube	6.54e-12	40
regional part of forebrain	2.09e-11	39
forebrain	2.09e-11	39
future forebrain	2.09e-11	39
regional part of brain	2.29e-11	46
brain grey matter	9.91e-10	29
regional part of telencephalon	9.91e-10	29
telencephalon	9.91e-10	29
structure with developmental contribution from neural crest	5.69e-09	92

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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