MCL coexpression mm9:2210

Phase1 CAGE Peaks

	Short description
Mm9::chr17:36408377..36408428,+	p@chr17:36408377..36408428 +
Mm9::chr18:6490776..6490791,-	p6@Epc1
Mm9::chr18:6490806..6490867,-	p1@Epc1
Mm9::chr7:80703273..80703291,-	p1@1810026B05Rik

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:0051149	positive regulation of muscle cell differentiation	0.00531419492686134
GO:0051155	positive regulation of striated muscle cell differentiation	0.00531419492686134
GO:0051153	regulation of striated muscle cell differentiation	0.00531419492686134
GO:0051147	regulation of muscle cell differentiation	0.00531419492686134
GO:0045814	negative regulation of gene expression, epigenetic	0.015942584780584
GO:0051146	striated muscle cell differentiation	0.0256852754798298
GO:0040029	regulation of gene expression, epigenetic	0.0305566208294527
GO:0045597	positive regulation of cell differentiation	0.0305566208294527
GO:0031965	nuclear membrane	0.0333344954503121
GO:0042692	muscle cell differentiation	0.0333344954503121
GO:0051094	positive regulation of developmental process	0.0333344954503121
GO:0001558	regulation of cell growth	0.0358708157563141
GO:0016049	cell growth	0.0382622034734017
GO:0008361	regulation of cell size	0.0382622034734017
GO:0005635	nuclear envelope	0.0382622034734017
GO:0014706	striated muscle development	0.0405207363173177
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0420074456123325
GO:0040008	regulation of growth	0.0420074456123325
GO:0045595	regulation of cell differentiation	0.0420074456123325
GO:0016568	chromatin modification	0.0420074456123325
GO:0007517	muscle development	0.0420074456123325
GO:0045892	negative regulation of transcription, DNA-dependent	0.0451706568783214
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0455172348083341
GO:0045893	positive regulation of transcription, DNA-dependent	0.0470225732922276
GO:0016481	negative regulation of transcription	0.0470225732922276
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0470225732922276
GO:0050793	regulation of developmental process	0.0470225732922276
GO:0006325	establishment and/or maintenance of chromatin architecture	0.0470225732922276
GO:0006323	DNA packaging	0.0470225732922276
GO:0045941	positive regulation of transcription	0.0470225732922276
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0470225732922276
GO:0012505	endomembrane system	0.0470225732922276
GO:0031324	negative regulation of cellular metabolic process	0.0470225732922276

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
mature alpha-beta T cell	3.27e-07	9
alpha-beta T cell	3.27e-07	9
immature T cell	3.27e-07	9
mature T cell	3.27e-07	9
immature alpha-beta T cell	3.27e-07	9

Uber Anatomy

Ontology term	p-value	n
anterior region of body	5.23e-12	43
craniocervical region	3.47e-11	36
gland of gut	1.21e-08	24
respiratory system	1.31e-08	42
thymus	1.62e-08	23
neck	1.62e-08	23
respiratory system epithelium	1.62e-08	23
hemolymphoid system gland	1.62e-08	23
pharyngeal epithelium	1.62e-08	23
thymic region	1.62e-08	23
pharyngeal gland	1.62e-08	23
entire pharyngeal arch endoderm	1.62e-08	23
thymus primordium	1.62e-08	23
early pharyngeal endoderm	1.62e-08	23
respiratory tract	1.90e-08	41
pharynx	4.09e-08	24
upper respiratory tract	4.09e-08	24
chordate pharynx	4.09e-08	24
pharyngeal arch system	4.09e-08	24
pharyngeal region of foregut	4.09e-08	24
hemopoietic organ	2.13e-07	29
immune organ	2.13e-07	29

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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