Coexpression cluster:C2536

Full id: C2536_cervix_occipital_breast_parietal_uterus_smooth_temporal

Phase1 CAGE Peaks

Hg19::chr1:164528340..164528379,+	p4@PBX1
Hg19::chr1:164528384..164528409,+	p3@PBX1
Hg19::chr1:164528410..164528428,+	p1@PBX1
Hg19::chr1:164528445..164528459,+	p2@PBX1

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	2.63e-39	115
central nervous system	9.45e-27	82
regional part of nervous system	5.01e-25	94
nervous system	5.01e-25	94
neurectoderm	4.18e-23	90
ectoderm	5.64e-23	173
presumptive ectoderm	5.64e-23	173
neural plate	7.74e-23	86
presumptive neural plate	7.74e-23	86
brain	9.15e-23	69
future brain	9.15e-23	69
ectoderm-derived structure	1.67e-22	169
neural tube	1.72e-22	57
neural rod	1.72e-22	57
future spinal cord	1.72e-22	57
neural keel	1.72e-22	57
regional part of brain	4.14e-22	59
multi-tissue structure	2.47e-21	347
organism subdivision	3.32e-21	365
multi-cellular organism	9.91e-20	659
head	1.29e-19	123
anterior neural tube	4.08e-19	42
anterior region of body	4.71e-19	129
craniocervical region	4.71e-19	129
regional part of forebrain	1.18e-18	41
forebrain	1.18e-18	41
future forebrain	1.18e-18	41
pre-chordal neural plate	4.14e-18	61
telencephalon	1.76e-16	34
anatomical cluster	2.05e-16	286
cerebral hemisphere	3.54e-16	32
organ part	4.33e-16	219
regional part of telencephalon	6.09e-16	33
gray matter	6.73e-16	34
brain grey matter	6.73e-16	34
cerebral cortex	5.79e-14	25
pallium	5.79e-14	25
anatomical group	6.95e-14	626
anatomical system	9.62e-14	625
regional part of cerebral cortex	2.11e-13	22
organ	2.51e-13	511
embryo	3.34e-13	612
anatomical conduit	3.70e-13	241
cell layer	8.61e-13	312
neocortex	1.44e-12	20
epithelium	1.44e-12	309
embryonic structure	6.82e-12	605
developing anatomical structure	6.82e-12	605
germ layer	1.61e-11	604
embryonic tissue	1.61e-11	604
presumptive structure	1.61e-11	604
epiblast (generic)	1.61e-11	604
tube	3.36e-11	194
organ segment	5.63e-07	97

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
CEBPB#1051	4	7.97114762582482	0.000247638578809083	0.00268178406597281
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000722048703980846
GTF2F1#2962	4	12.7396608767577	3.79492332235515e-05	0.000718524287279641
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00307638541152266
MXI1#4601	4	9.9615716287593	0.000101522475495045	0.00142435596698374
NFYA#4800	4	18.4255806998305	8.67100748407158e-06	0.000234487661996104
NFYB#4801	4	16.7597932535365	1.26678572070404e-05	0.000311444995020267
PBX3#5090	4	21.9145126867441	4.33289161192893e-06	0.000136466485843862
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00129430051688299
SP2#6668	4	26.1535304938446	2.13562021071447e-06	7.74720525136537e-05
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322384282381146
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140353304782599
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244355878693406
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00248963911819684

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.