MCL coexpression mm9:540

Phase1 CAGE Peaks

	Short description
Mm9::chr13:14156043..14156089,+	p1@Arid4b
Mm9::chr14:55305442..55305484,-	p1@Acin1
Mm9::chr16:91648104..91648150,+	p1@Son
Mm9::chr17:21145885..21145977,+	p1@Zfp160
Mm9::chr1:13364108..13364150,-	p1@Ncoa2
Mm9::chr2:90585696..90585760,+	p1@Fnbp4
Mm9::chr3:103718483..103718528,+	p1@Rsbn1
Mm9::chr4:33397281..33397362,+	p1@Rngtt
Mm9::chr4:97439116..97439202,+	p5@Nfia
Mm9::chr5:28643693..28643760,+	p1@Rbm33
Mm9::chr5:87233239..87233301,+	p1@Ythdc1
Mm9::chr5:87233329..87233344,+	p3@Ythdc1
Mm9::chr7:97591284..97591375,+	p1@Crebzf
Mm9::chr9:3404058..3404098,+	p1@Cwf19l2

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:0005634	nucleus	0.0048379566785366
GO:0003676	nucleic acid binding	0.0163873355820728
GO:0008192	RNA guanylyltransferase activity	0.0163873355820728
GO:0004651	polynucleotide 5'-phosphatase activity	0.0163873355820728
GO:0004484	mRNA guanylyltransferase activity	0.0163873355820728
GO:0016070	RNA metabolic process	0.0163873355820728
GO:0019204	nucleotide phosphatase activity	0.0163873355820728
GO:0006370	mRNA capping	0.0163873355820728
GO:0009452	RNA capping	0.0163873355820728
GO:0030375	thyroid hormone receptor coactivator activity	0.0163873355820728
GO:0043231	intracellular membrane-bound organelle	0.0183524153970818
GO:0043227	membrane-bound organelle	0.0183524153970818
GO:0010467	gene expression	0.0220637460588127
GO:0006355	regulation of transcription, DNA-dependent	0.0220637460588127
GO:0006351	transcription, DNA-dependent	0.0220637460588127
GO:0032774	RNA biosynthetic process	0.0220637460588127
GO:0003677	DNA binding	0.0220637460588127
GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	0.0220637460588127
GO:0045449	regulation of transcription	0.0220637460588127
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0228643097388343
GO:0006350	transcription	0.0230680736278133
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0232827137626862
GO:0010468	regulation of gene expression	0.0238818840034528
GO:0043229	intracellular organelle	0.0238818840034528
GO:0043226	organelle	0.0238818840034528
GO:0031323	regulation of cellular metabolic process	0.0257273200703863
GO:0019222	regulation of metabolic process	0.0290358876100918
GO:0035257	nuclear hormone receptor binding	0.0321101553567733
GO:0051427	hormone receptor binding	0.0338120948335617
GO:0030518	steroid hormone receptor signaling pathway	0.0353990829736296
GO:0030522	intracellular receptor-mediated signaling pathway	0.0473681302617389

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
anterior region of body	5.56e-10	43
craniocervical region	2.46e-09	36
respiratory system	5.52e-09	42
respiratory tract	6.58e-09	41
hemopoietic organ	1.17e-08	29
immune organ	1.17e-08	29
gland of gut	1.98e-08	24
thymus	2.08e-08	23
neck	2.08e-08	23
respiratory system epithelium	2.08e-08	23
hemolymphoid system gland	2.08e-08	23
pharyngeal epithelium	2.08e-08	23
thymic region	2.08e-08	23
pharyngeal gland	2.08e-08	23
entire pharyngeal arch endoderm	2.08e-08	23
thymus primordium	2.08e-08	23
early pharyngeal endoderm	2.08e-08	23
pharynx	5.41e-08	24
upper respiratory tract	5.41e-08	24
chordate pharynx	5.41e-08	24
pharyngeal arch system	5.41e-08	24
pharyngeal region of foregut	5.41e-08	24
mixed endoderm/mesoderm-derived structure	3.82e-07	35

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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