Coexpression cluster:C2486

Full id: C2486_optic_Adipocyte_aorta_embryonic_diencephalon_basal_corpus

Phase1 CAGE Peaks

Hg19::chr19:38743538..38743565,+	p@chr19:38743538..38743565 +
Hg19::chr19:38746979..38747050,-	p1@PPP1R14A
Hg19::chr19:38747153..38747169,-	p3@PPP1R14A
Hg19::chr19:38747174..38747218,-	p2@PPP1R14A

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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No GOStat results

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	9.45e-40	115
neural tube	5.47e-22	57
neural rod	5.47e-22	57
future spinal cord	5.47e-22	57
neural keel	5.47e-22	57
regional part of brain	1.22e-20	59
neural plate	1.07e-19	86
presumptive neural plate	1.07e-19	86
central nervous system	1.17e-17	82
neurectoderm	1.38e-17	90
regional part of nervous system	2.77e-17	94
nervous system	2.77e-17	94
organism subdivision	6.64e-17	365
anterior neural tube	6.17e-16	42
brain	1.20e-15	69
future brain	1.20e-15	69
regional part of forebrain	1.55e-15	41
forebrain	1.55e-15	41
future forebrain	1.55e-15	41
gray matter	7.84e-15	34
brain grey matter	7.84e-15	34
telencephalon	8.49e-15	34
pre-chordal neural plate	1.15e-14	61
ectoderm-derived structure	1.15e-14	169
regional part of telencephalon	3.08e-14	33
head	5.46e-14	123
cell layer	7.09e-14	312
tube	1.02e-13	194
ectoderm	1.63e-13	173
presumptive ectoderm	1.63e-13	173
cerebral hemisphere	1.67e-13	32
anatomical conduit	2.25e-13	241
epithelium	2.25e-13	309
anterior region of body	4.70e-13	129
craniocervical region	4.70e-13	129
multi-tissue structure	2.98e-12	347
organ part	1.15e-11	219
anatomical cluster	1.55e-11	286
cerebral cortex	6.55e-10	25
pallium	6.55e-10	25
regional part of cerebral cortex	7.01e-10	22
neocortex	5.73e-09	20
anatomical space	1.41e-08	104
multi-cellular organism	3.09e-08	659
anatomical cavity	6.06e-08	70
body cavity precursor	1.04e-07	63
compound organ	1.53e-07	69
posterior neural tube	2.63e-07	15
chordal neural plate	2.63e-07	15
immaterial anatomical entity	4.65e-07	126

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
CTCFL#140690	3	14.8098557692308	0.000499629176756334	0.00440902168071438
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0282953661992473
NR3C1#2908	3	11.2297674983798	0.00113167206806385	0.00775478637336926
NRF1#4899	3	9.15770958578318	0.00206195379173342	0.0119624703952254
RAD21#5885	3	7.76627542159225	0.003341119385872	0.0172675755909089
SMC3#9126	3	11.2836996336996	0.00111580236686805	0.00765658892203238
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342459922464406

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.