Coexpression cluster:C4698

Full id: C4698_spinal_heart_esophagus_trachea_duodenum_substantia_penis

Phase1 CAGE Peaks

Hg19::chr7:7575477..7575491,-	p2@COL28A1
Hg19::chr7:7575494..7575509,-	p1@COL28A1
Hg19::chrX:31526382..31526422,-	p10@DMD

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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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0043034	costamere	0.00824159647213382
GO:0043043	peptide biosynthetic process	0.00824159647213382
GO:0016010	dystrophin-associated glycoprotein complex	0.0230639023484972
GO:0006518	peptide metabolic process	0.0230639023484972
GO:0005605	basal lamina	0.0230639023484972
GO:0008307	structural constituent of muscle	0.0230639023484972
GO:0030016	myofibril	0.023422404691628
GO:0044449	contractile fiber part	0.023422404691628
GO:0043292	contractile fiber	0.023422404691628
GO:0005604	basement membrane	0.0243703490898033
GO:0005200	structural constituent of cytoskeleton	0.0254440286675898
GO:0044420	extracellular matrix part	0.0353517517207721
GO:0003012	muscle system process	0.0353517517207721
GO:0006936	muscle contraction	0.0353517517207721
GO:0004867	serine-type endopeptidase inhibitor activity	0.0353517517207721
GO:0007517	muscle development	0.0353517517207721
GO:0004866	endopeptidase inhibitor activity	0.0485298345557758
GO:0030414	protease inhibitor activity	0.0485298345557758

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
adult organism	3.59e-65	115
neural tube	4.83e-25	57
neural rod	4.83e-25	57
future spinal cord	4.83e-25	57
neural keel	4.83e-25	57
neural plate	1.19e-21	86
presumptive neural plate	1.19e-21	86
central nervous system	8.78e-21	82
neurectoderm	3.95e-20	90
regional part of brain	1.15e-18	59
regional part of nervous system	1.34e-17	94
nervous system	1.34e-17	94
anterior neural tube	1.49e-15	42
brain	2.21e-15	69
future brain	2.21e-15	69
regional part of forebrain	1.29e-14	41
forebrain	1.29e-14	41
future forebrain	1.29e-14	41
gray matter	1.32e-12	34
brain grey matter	1.32e-12	34
ectoderm-derived structure	1.49e-12	169
telencephalon	1.65e-12	34
brainstem	2.40e-12	8
ectoderm	6.12e-12	173
presumptive ectoderm	6.12e-12	173
regional part of telencephalon	9.30e-12	33
anterior region of body	2.10e-11	129
craniocervical region	2.10e-11	129
posterior neural tube	2.98e-11	15
chordal neural plate	2.98e-11	15
multi-tissue structure	3.19e-11	347
anatomical conduit	5.28e-11	241
cerebral hemisphere	1.61e-10	32
head	3.51e-10	123
organ	3.79e-10	511
pre-chordal neural plate	8.74e-10	61
anatomical cluster	1.61e-09	286
tube	2.12e-09	194
cerebral cortex	8.66e-09	25
pallium	8.66e-09	25
compound organ	1.63e-08	69
multi-cellular organism	2.90e-08	659
anatomical system	1.08e-07	625
anatomical group	1.23e-07	626
embryo	1.27e-07	612
primary circulatory organ	3.21e-07	27
segmental subdivision of hindbrain	3.96e-07	12
hindbrain	3.96e-07	12
presumptive hindbrain	3.96e-07	12
embryonic structure	4.76e-07	605
developing anatomical structure	4.76e-07	605

Overrepresented TFBS (DNA) motifs on this co-expression cluster<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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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.