Coexpression cluster:C3164

Full id: C3164_pharyngeal_temporal_occipital_Hepatocyte_rectum_optic_brain

Phase1 CAGE Peaks

Hg19::chr11:58939589..58939610,+	p3@DTX4
Hg19::chr11:58939616..58939668,+	p1@DTX4
Hg19::chr11:58939673..58939697,+	p2@DTX4

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	3.67e-22	115
neural tube	1.51e-18	57
neural rod	1.51e-18	57
future spinal cord	1.51e-18	57
neural keel	1.51e-18	57
central nervous system	3.46e-16	82
neural plate	1.28e-15	86
presumptive neural plate	1.28e-15	86
regional part of brain	5.11e-15	59
anterior neural tube	4.14e-14	42
neurectoderm	4.54e-14	90
regional part of forebrain	4.78e-14	41
forebrain	4.78e-14	41
future forebrain	4.78e-14	41
subdivision of digestive tract	2.67e-13	129
endodermal part of digestive tract	2.67e-13	129
regional part of nervous system	3.24e-13	94
nervous system	3.24e-13	94
organ part	5.12e-13	219
endoderm-derived structure	8.10e-13	169
endoderm	8.10e-13	169
presumptive endoderm	8.10e-13	169
telencephalon	9.47e-13	34
gray matter	1.86e-12	34
brain grey matter	1.86e-12	34
regional part of telencephalon	2.83e-12	33
brain	4.97e-12	69
future brain	4.97e-12	69
ectoderm-derived structure	6.66e-12	169
cerebral hemisphere	8.28e-12	32
digestive system	8.39e-12	155
digestive tract	8.39e-12	155
primitive gut	8.39e-12	155
pre-chordal neural plate	1.69e-11	61
ectoderm	4.65e-11	173
presumptive ectoderm	4.65e-11	173
regional part of cerebral cortex	1.20e-10	22
cerebral cortex	3.07e-10	25
pallium	3.07e-10	25
organ	5.54e-10	511
neocortex	5.65e-10	20
head	6.67e-10	123
anterior region of body	1.94e-09	129
craniocervical region	1.94e-09	129
multi-tissue structure	2.00e-09	347
mixed endoderm/mesoderm-derived structure	5.81e-09	130
gastrointestinal system	3.41e-08	35
embryo	4.21e-07	612

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278434350531653
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171191357010173
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032054753212157
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268641630855191
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172358153812209
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00879679973020348
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00662018873751301
SMARCC1#6599	3	43.6633593196315	1.20046018043203e-05	0.000300947817532743
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308093519974093
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0108820016175891
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328055799078333
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.013963615610628
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00387785859559917

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.