Coexpression cluster:C522

Full id: C522_pituitary_medulla_lung_testis_caudate_epididymis_thyroid

Phase1 CAGE Peaks

Hg19::chr10:119806476..119806520,+	p1@CASC2
Hg19::chr10:75118471..75118533,-	p1@TTC18
Hg19::chr11:101785727..101785767,+	p1@KIAA1377
Hg19::chr11:102980126..102980199,+	p2@DYNC2H1
Hg19::chr16:71598823..71598868,-	p@chr16:71598823..71598868 -
Hg19::chr17:78388884..78388946,-	p1@uc002jyi.1
Hg19::chr1:151693984..151694016,+	p1@RIIAD1
Hg19::chr1:169396646..169396660,-	p2@C1orf114
Hg19::chr1:42928945..42929017,+	p1@CCDC30
Hg19::chr22:44208137..44208219,-	p1@EFCAB6
Hg19::chr2:196933548..196933601,-	p1@DNAH7
Hg19::chr3:119421849..119421962,+	p1@C3orf15
Hg19::chr3:130745688..130745761,+	p1@NEK11
Hg19::chr5:110074603..110074661,-	p1@TMEM232
Hg19::chr6:163149104..163149130,+	p3@PACRG
Hg19::chr9:34458771..34458850,+	p1@DNAI1
Hg19::chrX:35937879..35937902,+	p1@CXorf22

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:0030286	dynein complex	1.51318584945636e-05
GO:0005875	microtubule associated complex	0.00050209970312256
GO:0015630	microtubule cytoskeleton	0.00772417870359773
GO:0003777	microtubule motor activity	0.0147235821100474
GO:0044430	cytoskeletal part	0.0245198976747638
GO:0031573	intra-S DNA damage checkpoint	0.0245198976747638
GO:0042995	cell projection	0.0339156691283648
GO:0001539	ciliary or flagellar motility	0.0339156691283648
GO:0043232	intracellular non-membrane-bound organelle	0.0339156691283648
GO:0043228	non-membrane-bound organelle	0.0339156691283648
GO:0005858	axonemal dynein complex	0.0339156691283648
GO:0005856	cytoskeleton	0.0339156691283648
GO:0044447	axoneme part	0.0339156691283648
GO:0005930	axoneme	0.041969206624181
GO:0000077	DNA damage checkpoint	0.0489388637877478

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	4.46e-34	114
nervous system	1.22e-33	89
central nervous system	2.44e-33	81
neural tube	1.79e-31	56
neural rod	1.79e-31	56
future spinal cord	1.79e-31	56
neural keel	1.79e-31	56
regional part of nervous system	1.02e-29	53
regional part of brain	1.02e-29	53
neurectoderm	3.65e-29	86
brain	1.84e-28	68
future brain	1.84e-28	68
neural plate	3.44e-28	82
presumptive neural plate	3.44e-28	82
ectoderm-derived structure	3.53e-26	171
ectoderm	3.53e-26	171
presumptive ectoderm	3.53e-26	171
organ system subdivision	3.60e-26	223
regional part of forebrain	7.84e-26	41
forebrain	7.84e-26	41
anterior neural tube	7.84e-26	41
future forebrain	7.84e-26	41
pre-chordal neural plate	4.41e-22	61
brain grey matter	2.95e-21	34
gray matter	2.95e-21	34
telencephalon	3.80e-21	34
ecto-epithelium	1.66e-20	104
cerebral hemisphere	4.21e-20	32
regional part of telencephalon	6.26e-20	32
structure with developmental contribution from neural crest	1.16e-19	132
cerebral cortex	8.51e-16	25
pallium	8.51e-16	25
regional part of cerebral cortex	6.94e-15	22
anatomical cluster	2.01e-14	373
neocortex	1.19e-13	20
multi-tissue structure	1.12e-12	342
organ	1.37e-09	503
organ part	2.61e-09	218
posterior neural tube	5.26e-07	15
chordal neural plate	5.26e-07	15
neural nucleus	6.35e-07	9
nucleus of brain	6.35e-07	9
basal ganglion	7.07e-07	9
nuclear complex of neuraxis	7.07e-07	9
aggregate regional part of brain	7.07e-07	9
collection of basal ganglia	7.07e-07	9
cerebral subcortex	7.07e-07	9

Disease

Ontology term	p-value	n
cell type cancer	1.15e-07	143

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
ATF3#467	4	5.28545282964912	0.00585762962104294	0.0262932470878112
CCNT2#905	8	2.98174191857065	0.00243014541697788	0.0136886876222292
E2F1#1869	11	3.17536949198074	9.04802704927931e-05	0.00132015492735357
ELF1#1997	11	2.755239855699	0.000348982991074966	0.00352353389451647
GABPB1#2553	11	4.57320718811788	2.44871881059722e-06	8.65454293942346e-05
HEY1#23462	9	2.13888231693832	0.0115734531098334	0.0422895482939574
MAX#4149	8	3.036496710121	0.00215601866543559	0.0124439034760667
MXI1#4601	10	5.85974801691723	1.03431706779201e-06	4.31746763561669e-05
NR2C2#7182	3	5.7555195715131	0.0141956977999394	0.0497979471492634
NRF1#4899	7	5.02776212552802	0.000229274601716291	0.0025282663001423
PAX5#5079	8	3.13861907349545	0.00173212486138333	0.0106619548769973
POLR2A#5430	15	1.89481162637477	0.00045412137082633	0.00422069785954713
RFX5#5993	6	4.25220382136298	0.00180848049643333	0.0109385472037412
SIN3A#25942	14	4.45437565737717	2.0970960182552e-08	1.48890966043885e-06
SP1#6667	8	2.68159123677219	0.00482897247791604	0.0226564715463196
SPI1#6688	6	2.89564359124332	0.0122532128785811	0.0444206081372532
SREBF1#6720	5	13.8252498354377	2.17206571175176e-05	0.000478179533873613
TAF1#6872	13	2.55644715968758	9.98053131212947e-05	0.00140460410956406
TBP#6908	11	2.3984986798859	0.00125412277486403	0.0084290706277125
USF1#7391	7	2.61944087885034	0.0107062462329532	0.0395231575526988
YY1#7528	11	3.1778163675525	8.98110145449078e-05	0.00131130610206286
ZEB1#6935	7	6.95406024251806	2.9174422587585e-05	0.000609999503628587
ZNF263#10127	6	2.90182646012142	0.0121295164888246	0.0439813412691857

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.