MCL coexpression mm9:1095

Phase1 CAGE Peaks

	Short description
Mm9::chr11:96164887..96164894,+	p4@Hoxb5
Mm9::chr11:96164905..96164919,+	p2@Hoxb5
Mm9::chr11:96164928..96164947,+	p@chr11:96164928..96164947 +
Mm9::chr11:96164964..96165032,+	p@chr11:96164964..96165032 +
Mm9::chr11:96165039..96165073,+	p@chr11:96165039..96165073 +
Mm9::chr6:52114447..52114463,-	p@chr6:52114447..52114463 -
Mm9::chr6:52114472..52114489,-	p@chr6:52114472..52114489 -

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:0007389	pattern specification process	0.00704628605978155
GO:0048703	embryonic viscerocranium morphogenesis	0.00704628605978155
GO:0005667	transcription factor complex	0.00704628605978155
GO:0043565	sequence-specific DNA binding	0.00704628605978155
GO:0048701	embryonic cranial skeleton morphogenesis	0.00704628605978155
GO:0042474	middle ear morphogenesis	0.00704628605978155
GO:0009887	organ morphogenesis	0.00704628605978155
GO:0044451	nucleoplasm part	0.00704628605978155
GO:0005654	nucleoplasm	0.00704628605978155
GO:0045446	endothelial cell differentiation	0.00746882169324845
GO:0048704	embryonic skeletal morphogenesis	0.00746882169324845
GO:0031981	nuclear lumen	0.00746882169324845
GO:0031974	membrane-enclosed lumen	0.00814543077564118
GO:0043233	organelle lumen	0.00814543077564118
GO:0048706	embryonic skeletal development	0.00829476945773949
GO:0003700	transcription factor activity	0.00859934249097884
GO:0048705	skeletal morphogenesis	0.0103661885975155
GO:0001709	cell fate determination	0.0103661885975155
GO:0044428	nuclear part	0.010608137469431
GO:0009653	anatomical structure morphogenesis	0.013093475674337
GO:0048513	organ development	0.0177494802129741
GO:0042471	ear morphogenesis	0.0211826435861262
GO:0043234	protein complex	0.0221767273126586
GO:0048731	system development	0.0221767273126586
GO:0043583	ear development	0.0221767273126586
GO:0048869	cellular developmental process	0.0221767273126586
GO:0030154	cell differentiation	0.0221767273126586
GO:0006355	regulation of transcription, DNA-dependent	0.0221767273126586
GO:0006351	transcription, DNA-dependent	0.0221767273126586
GO:0032774	RNA biosynthetic process	0.0221767273126586
GO:0003677	DNA binding	0.0221767273126586
GO:0045449	regulation of transcription	0.0221767273126586
GO:0048856	anatomical structure development	0.0221767273126586
GO:0045165	cell fate commitment	0.0221767273126586
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0221767273126586
GO:0006350	transcription	0.0221767273126586
GO:0032991	macromolecular complex	0.0221835585063547
GO:0010468	regulation of gene expression	0.022444354649964
GO:0031323	regulation of cellular metabolic process	0.0236983998555817
GO:0007275	multicellular organismal development	0.0241833631015704
GO:0019222	regulation of metabolic process	0.0242401984828042
GO:0016070	RNA metabolic process	0.0249287093220019
GO:0044446	intracellular organelle part	0.0254998168855322
GO:0044422	organelle part	0.0254998168855322
GO:0001501	skeletal development	0.0309655821500028
GO:0007423	sensory organ development	0.031296994214026
GO:0010467	gene expression	0.031902634374277
GO:0048598	embryonic morphogenesis	0.0320949688724849
GO:0003676	nucleic acid binding	0.0320949688724849
GO:0032502	developmental process	0.0333071565541416
GO:0043009	chordate embryonic development	0.0333071565541416
GO:0009792	embryonic development ending in birth or egg hatching	0.0333071565541416
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0344612923443434
GO:0050794	regulation of cellular process	0.0388992151408601
GO:0050789	regulation of biological process	0.0473715943392161

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
lung	6.83e-12	14
respiratory tube	6.83e-12	14
respiration organ	6.83e-12	14
pair of lungs	6.83e-12	14
lung primordium	6.83e-12	14
lung bud	6.83e-12	14
epithelial fold	1.70e-11	20
thoracic cavity element	7.83e-10	17
thoracic segment organ	7.83e-10	17
thoracic cavity	7.83e-10	17
thoracic segment of trunk	7.83e-10	17
respiratory primordium	7.83e-10	17
endoderm of foregut	7.83e-10	17
epithelial bud	8.23e-09	17

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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