Coexpression cluster:C3026

Full id: C3026_medulla_aorta_optic_spinal_locus_corpus_skeletal

Phase1 CAGE Peaks

Hg19::chr10:5454633..5454661,+	p4@NET1
Hg19::chr10:5454672..5454689,+	p1@CU690984
Hg19::chr4:79892654..79892672,+	p5@LOC100505875

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:0005089	Rho guanyl-nucleotide exchange factor activity	0.0288031319910514
GO:0035023	regulation of Rho protein signal transduction	0.0288031319910514
GO:0001558	regulation of cell growth	0.0288031319910514
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0288031319910514
GO:0007266	Rho protein signal transduction	0.0288031319910514
GO:0016049	cell growth	0.0288031319910514
GO:0040008	regulation of growth	0.0288031319910514
GO:0008361	regulation of cell size	0.0288031319910514
GO:0005085	guanyl-nucleotide exchange factor activity	0.0356450410141685
GO:0046578	regulation of Ras protein signal transduction	0.0356450410141685
GO:0007265	Ras protein signal transduction	0.0356450410141685
GO:0005083	small GTPase regulator activity	0.0356450410141685
GO:0051056	regulation of small GTPase mediated signal transduction	0.0356450410141685
GO:0032989	cellular structure morphogenesis	0.0356450410141685
GO:0000902	cell morphogenesis	0.0356450410141685
GO:0030695	GTPase regulator activity	0.0489373601789709

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	5.91e-43	115
neural tube	2.61e-31	57
neural rod	2.61e-31	57
future spinal cord	2.61e-31	57
neural keel	2.61e-31	57
central nervous system	4.58e-31	82
regional part of nervous system	2.40e-29	94
nervous system	2.40e-29	94
brain	2.66e-27	69
future brain	2.66e-27	69
regional part of brain	1.70e-26	59
anterior neural tube	1.81e-23	42
neural plate	1.81e-23	86
presumptive neural plate	1.81e-23	86
regional part of forebrain	8.73e-23	41
forebrain	8.73e-23	41
future forebrain	8.73e-23	41
ectoderm-derived structure	1.17e-22	169
neurectoderm	1.98e-22	90
ectoderm	3.73e-22	173
presumptive ectoderm	3.73e-22	173
head	5.16e-22	123
anterior region of body	2.05e-21	129
craniocervical region	2.05e-21	129
gray matter	3.64e-19	34
brain grey matter	3.64e-19	34
telencephalon	5.13e-19	34
regional part of telencephalon	1.80e-18	33
organism subdivision	1.13e-17	365
cerebral hemisphere	1.22e-17	32
pre-chordal neural plate	5.59e-16	61
multi-tissue structure	1.24e-14	347
cerebral cortex	6.38e-14	25
pallium	6.38e-14	25
anatomical cluster	3.69e-13	286
regional part of cerebral cortex	7.13e-13	22
organ	1.76e-12	511
anatomical conduit	4.24e-12	241
neocortex	1.25e-11	20
tube	2.80e-10	194
multi-cellular organism	1.33e-09	659
anatomical system	2.24e-09	625
anatomical group	3.58e-09	626
posterior neural tube	6.43e-09	15
chordal neural plate	6.43e-09	15
embryo	2.09e-08	612
epithelium	2.30e-08	309
embryonic structure	2.87e-08	605
developing anatomical structure	2.87e-08	605
cell layer	3.19e-08	312
germ layer	4.50e-08	604
embryonic tissue	4.50e-08	604
presumptive structure	4.50e-08	604
epiblast (generic)	4.50e-08	604
segmental subdivision of nervous system	1.36e-07	13
organ part	2.56e-07	219
brainstem	4.25e-07	8
segmental subdivision of hindbrain	6.34e-07	12
hindbrain	6.34e-07	12
presumptive hindbrain	6.34e-07	12
nucleus of brain	9.58e-07	9
neural nucleus	9.58e-07	9

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.