MCL coexpression mm9:1831

Phase1 CAGE Peaks

	Short description
Mm9::chr6:6812839..6812856,-	p@chr6:6812839..6812856 -
Mm9::chr6:6812962..6812979,+	p1@Dlx6
Mm9::chr6:6812988..6813002,+	p3@Dlx6
Mm9::chr6:6813269..6813272,+	p2@Dlx6
Mm9::chr6:6832076..6832092,-	p1@Dlx5

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

---

GO ID	GO name	FDR corrected p-value
GO:0030326	embryonic limb morphogenesis	0.000258943501150261
GO:0035113	embryonic appendage morphogenesis	0.000258943501150261
GO:0035107	appendage morphogenesis	0.000258943501150261
GO:0035108	limb morphogenesis	0.000258943501150261
GO:0048736	appendage development	0.000258943501150261
GO:0060173	limb development	0.000258943501150261
GO:0048598	embryonic morphogenesis	0.0014479800732008
GO:0005667	transcription factor complex	0.00502663040665224
GO:0043565	sequence-specific DNA binding	0.00502663040665224
GO:0009790	embryonic development	0.00502663040665224
GO:0044451	nucleoplasm part	0.0062098763682065
GO:0005654	nucleoplasm	0.00625233833473574
GO:0031981	nuclear lumen	0.00815663300844468
GO:0031974	membrane-enclosed lumen	0.00899439116634181
GO:0043233	organelle lumen	0.00899439116634181
GO:0003700	transcription factor activity	0.0101738699893271
GO:0044428	nuclear part	0.0140269986754033
GO:0009653	anatomical structure morphogenesis	0.0172120806986589
GO:0042472	inner ear morphogenesis	0.0261206619311803
GO:0042471	ear morphogenesis	0.0275672713712403
GO:0043234	protein complex	0.0291253627649331
GO:0048839	inner ear development	0.0292299925869118
GO:0043583	ear development	0.0303461707032352
GO:0006355	regulation of transcription, DNA-dependent	0.0303461707032352
GO:0006351	transcription, DNA-dependent	0.0303461707032352
GO:0032774	RNA biosynthetic process	0.0303461707032352
GO:0003677	DNA binding	0.0303461707032352
GO:0045449	regulation of transcription	0.0303461707032352
GO:0048856	anatomical structure development	0.0303461707032352
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0303461707032352
GO:0006350	transcription	0.0303461707032352
GO:0032991	macromolecular complex	0.0303461707032352
GO:0010468	regulation of gene expression	0.0305772001889394
GO:0031323	regulation of cellular metabolic process	0.0321607116515682
GO:0007275	multicellular organismal development	0.0326616758899756
GO:0019222	regulation of metabolic process	0.0326616758899756
GO:0016070	RNA metabolic process	0.0334786777647593
GO:0044446	intracellular organelle part	0.0340365919858891
GO:0044422	organelle part	0.0340365919858891
GO:0007409	axonogenesis	0.0352867503015634
GO:0048667	neuron morphogenesis during differentiation	0.0355616341903106
GO:0048812	neurite morphogenesis	0.0355616341903106
GO:0000904	cellular morphogenesis during differentiation	0.0387104947640834
GO:0007423	sensory organ development	0.0387104947640834
GO:0010467	gene expression	0.0388094600719565
GO:0031175	neurite development	0.0388094600719565
GO:0003676	nucleic acid binding	0.0395873215100833
GO:0032502	developmental process	0.0407048398569286
GO:0048666	neuron development	0.0407048398569286
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0432173728216949
GO:0032990	cell part morphogenesis	0.0460040440688511
GO:0030030	cell projection organization and biogenesis	0.0460040440688511
GO:0048858	cell projection morphogenesis	0.0460040440688511
GO:0050794	regulation of cellular process	0.0460040440688511
GO:0030182	neuron differentiation	0.0460040440688511

Relative expression of the co-expression cluster over median <br>Analyst:

---

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>

---

Uber Anatomy

Ontology term	p-value	n
anterior neural tube	3.09e-15	40
brain grey matter	3.14e-15	29
regional part of telencephalon	3.14e-15	29
telencephalon	3.14e-15	29
regional part of forebrain	5.24e-15	39
forebrain	5.24e-15	39
future forebrain	5.24e-15	39
brain	1.34e-12	47
future brain	1.34e-12	47
pre-chordal neural plate	8.14e-12	49
regional part of brain	8.51e-12	46
gray matter	1.25e-11	34
cerebral cortex	1.62e-10	21
cerebral hemisphere	1.62e-10	21
pallium	1.62e-10	21
regional part of nervous system	7.73e-10	54
neural tube	3.15e-09	52
neural rod	3.15e-09	52
future spinal cord	3.15e-09	52
neural keel	3.15e-09	52
regional part of cerebral cortex	6.47e-09	17
appendage	4.21e-08	12
paired limb/fin	4.21e-08	12
limb	4.21e-08	12
paired limb/fin bud	4.21e-08	12
limb bud	4.21e-08	12
limb/fin field	4.21e-08	12
limb field	4.21e-08	12
appendage girdle complex	3.30e-07	13

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

---

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}