MCL coexpression mm9:2011

Phase1 CAGE Peaks

	Short description
Mm9::chr11:96180069..96180089,+	p3@Hoxb4
Mm9::chr11:96213264..96213282,+	p5@Hoxb2
Mm9::chr11:96213288..96213332,+	p6@Hoxb2
Mm9::chr11:96213434..96213452,+	p7@Hoxb2

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	0.0067782216449032
GO:0005667	transcription factor complex	0.0067782216449032
GO:0043565	sequence-specific DNA binding	0.0067782216449032
GO:0048103	somatic stem cell division	0.0067782216449032
GO:0009887	organ morphogenesis	0.0067782216449032
GO:0044451	nucleoplasm part	0.0067782216449032
GO:0005654	nucleoplasm	0.0067782216449032
GO:0017145	stem cell division	0.0067782216449032
GO:0031981	nuclear lumen	0.00771427592729887
GO:0031974	membrane-enclosed lumen	0.00803070639851947
GO:0043233	organelle lumen	0.00803070639851947
GO:0003700	transcription factor activity	0.00888194999068237
GO:0044428	nuclear part	0.012010296484892
GO:0009653	anatomical structure morphogenesis	0.0144897618126466
GO:0048513	organ development	0.0192494362873099
GO:0043234	protein complex	0.0244547895776987
GO:0048731	system development	0.0244547895776987
GO:0006355	regulation of transcription, DNA-dependent	0.0244547895776987
GO:0006351	transcription, DNA-dependent	0.0244547895776987
GO:0032774	RNA biosynthetic process	0.0244547895776987
GO:0003677	DNA binding	0.0244547895776987
GO:0045449	regulation of transcription	0.0244547895776987
GO:0048856	anatomical structure development	0.0244547895776987
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0244547895776987
GO:0006350	transcription	0.0244547895776987
GO:0032991	macromolecular complex	0.0244547895776987
GO:0010468	regulation of gene expression	0.0244698493575507
GO:0031323	regulation of cellular metabolic process	0.0255699535665104
GO:0007275	multicellular organismal development	0.0256627453421236
GO:0019222	regulation of metabolic process	0.0256627453421236
GO:0016070	RNA metabolic process	0.0261632524006471
GO:0044446	intracellular organelle part	0.0263378390366999
GO:0044422	organelle part	0.0263378390366999
GO:0010467	gene expression	0.0341625144397291
GO:0003676	nucleic acid binding	0.0348072197631174
GO:0032502	developmental process	0.0360426389896548
GO:0051301	cell division	0.0372330122993926
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0372330122993926
GO:0050794	regulation of cellular process	0.041722885145668

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
trunk region element	1.18e-13	79
trunk	1.87e-13	90
subdivision of trunk	1.71e-11	66
cavitated compound organ	1.30e-10	21
epithelial fold	5.85e-10	20
lung	5.36e-09	14
respiratory tube	5.36e-09	14
respiration organ	5.36e-09	14
pair of lungs	5.36e-09	14
lung primordium	5.36e-09	14
lung bud	5.36e-09	14
thoracic cavity element	2.58e-08	17
thoracic segment organ	2.58e-08	17
thoracic cavity	2.58e-08	17
thoracic segment of trunk	2.58e-08	17
respiratory primordium	2.58e-08	17
endoderm of foregut	2.58e-08	17
epithelial bud	5.99e-08	17
kidney	2.04e-07	14
kidney mesenchyme	2.04e-07	14
upper urinary tract	2.04e-07	14
kidney rudiment	2.04e-07	14
kidney field	2.04e-07	14
anatomical space	6.60e-07	57
renal system	8.92e-07	19

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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