Coexpression cluster:C2996

Full id: C2996_optic_CD4_corpus_thalamus_globus_spinal_diencephalon

Phase1 CAGE Peaks

Hg19::chr10:14613932..14613943,-	p9@FAM107B
Hg19::chr10:14613968..14614048,-	p2@FAM107B
Hg19::chr5:80256453..80256506,+	p2@RASGRF2

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	0.0470387377840574
GO:0035023	regulation of Rho protein signal transduction	0.0470387377840574
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0470387377840574
GO:0007266	Rho protein signal transduction	0.0470387377840574

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	1.92e-20	18
alpha-beta T cell	1.92e-20	18
immature T cell	1.92e-20	18
mature T cell	1.92e-20	18
immature alpha-beta T cell	1.92e-20	18
CD8-positive, alpha-beta T cell	6.12e-15	11
T cell	5.20e-13	25
pro-T cell	5.20e-13	25
CD4-positive, alpha-beta T cell	1.06e-08	6

Uber Anatomy

Ontology term	p-value	n
adult organism	2.97e-60	114
neural tube	1.66e-36	56
neural rod	1.66e-36	56
future spinal cord	1.66e-36	56
neural keel	1.66e-36	56
regional part of nervous system	4.18e-33	53
regional part of brain	4.18e-33	53
regional part of forebrain	8.76e-27	41
forebrain	8.76e-27	41
anterior neural tube	8.76e-27	41
future forebrain	8.76e-27	41
brain	2.40e-26	68
future brain	2.40e-26	68
central nervous system	3.05e-26	81
telencephalon	1.12e-25	34
brain grey matter	2.74e-25	34
gray matter	2.74e-25	34
nervous system	2.22e-23	89
cerebral hemisphere	2.47e-23	32
regional part of telencephalon	3.38e-23	32
neural plate	1.99e-22	82
presumptive neural plate	1.99e-22	82
neurectoderm	1.17e-20	86
regional part of cerebral cortex	7.32e-19	22
neocortex	7.35e-17	20
cerebral cortex	6.93e-16	25
pallium	6.93e-16	25
pre-chordal neural plate	9.34e-16	61
ecto-epithelium	1.71e-14	104
organ system subdivision	3.87e-12	223
neural nucleus	1.89e-11	9
nucleus of brain	1.89e-11	9
basal ganglion	2.97e-11	9
nuclear complex of neuraxis	2.97e-11	9
aggregate regional part of brain	2.97e-11	9
collection of basal ganglia	2.97e-11	9
cerebral subcortex	2.97e-11	9
structure with developmental contribution from neural crest	6.84e-11	132
posterior neural tube	1.05e-10	15
chordal neural plate	1.05e-10	15
blood	7.21e-10	15
haemolymphatic fluid	7.21e-10	15
organism substance	7.21e-10	15
telencephalic nucleus	2.53e-09	7
segmental subdivision of nervous system	1.06e-08	13
brainstem	1.45e-08	6
gyrus	4.95e-08	6
tube	9.39e-08	192
segmental subdivision of hindbrain	1.60e-07	12
hindbrain	1.60e-07	12
presumptive hindbrain	1.60e-07	12
ectoderm-derived structure	4.08e-07	171
ectoderm	4.08e-07	171
presumptive ectoderm	4.08e-07	171
limbic system	9.97e-07	5

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)
{{{tfbs_overrepresentation_jaspar}}}

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BHLHE40#8553	2	29.9145423646516	0.00146748352710614	0.00939338760035785
ESR1#2099	2	20.5124021974363	0.00309974157709518	0.0163016219633538
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376536909768178
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0225747148711154
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.0189400269072109
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246675878099376
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.046005783090439
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298142891577996
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189421112955259

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.