Coexpression cluster:C4739

Full id: C4739_heart_vagina_bile_pineal_pancreas_lung_bladder

Phase1 CAGE Peaks

Hg19::chr8:17658704..17658715,-	p10@MTUS1
Hg19::chr8:17658721..17658766,-	p3@MTUS1
Hg19::chr8:17658793..17658804,-	p9@MTUS1

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>cell_data<br>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	1.39e-12	254
endodermal cell	2.18e-09	59
endo-epithelial cell	5.94e-07	43

Uber Anatomy

Ontology term	p-value	n
adult organism	8.41e-40	115
organ	1.21e-24	511
digestive system	1.10e-21	155
digestive tract	1.10e-21	155
primitive gut	1.10e-21	155
endoderm-derived structure	3.61e-21	169
endoderm	3.61e-21	169
presumptive endoderm	3.61e-21	169
multi-tissue structure	3.34e-20	347
subdivision of digestive tract	1.65e-18	129
endodermal part of digestive tract	1.65e-18	129
head	4.94e-18	123
anterior region of body	5.41e-18	129
craniocervical region	5.41e-18	129
neurectoderm	5.82e-17	90
neural plate	1.04e-16	86
presumptive neural plate	1.04e-16	86
neural tube	2.27e-16	57
neural rod	2.27e-16	57
future spinal cord	2.27e-16	57
neural keel	2.27e-16	57
multi-cellular organism	1.82e-15	659
ectoderm	4.19e-15	173
presumptive ectoderm	4.19e-15	173
embryo	5.61e-15	612
mixed endoderm/mesoderm-derived structure	7.37e-15	130
ectoderm-derived structure	9.91e-15	169
organ part	1.23e-14	219
central nervous system	2.10e-14	82
brain	4.49e-14	69
future brain	4.49e-14	69
anatomical system	5.79e-14	625
embryonic structure	6.55e-14	605
developing anatomical structure	6.55e-14	605
regional part of nervous system	9.02e-14	94
nervous system	9.02e-14	94
anatomical group	9.49e-14	626
anatomical cluster	1.08e-13	286
germ layer	1.30e-13	604
embryonic tissue	1.30e-13	604
presumptive structure	1.30e-13	604
epiblast (generic)	1.30e-13	604
regional part of brain	2.01e-13	59
organism subdivision	6.49e-13	365
anterior neural tube	3.22e-12	42
pre-chordal neural plate	5.11e-12	61
regional part of forebrain	1.04e-11	41
forebrain	1.04e-11	41
future forebrain	1.04e-11	41
foregut	1.39e-11	98
anatomical conduit	2.59e-11	241
primordium	2.32e-10	168
respiratory system	6.79e-10	72
endo-epithelium	8.25e-10	82
immaterial anatomical entity	1.73e-09	126
epithelium	4.88e-09	309
orifice	5.88e-09	35
gland	7.33e-09	59
cell layer	7.48e-09	312
gray matter	9.70e-09	34
brain grey matter	9.70e-09	34
telencephalon	1.54e-08	34
gut epithelium	2.52e-08	54
regional part of telencephalon	2.85e-08	33
trunk region element	4.16e-08	107
organ segment	6.82e-08	97
cerebral hemisphere	1.44e-07	32
epithelium of foregut-midgut junction	6.74e-07	25
anatomical boundary	6.74e-07	25
hepatobiliary system	6.74e-07	25
foregut-midgut junction	6.74e-07	25
septum transversum	6.74e-07	25
regional part of cerebral cortex	7.29e-07	22

Disease

Ontology term	p-value	n
carcinoma	5.62e-20	106
cell type cancer	3.32e-18	143
adenocarcinoma	1.05e-07	25
cancer	7.15e-07	235

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327887513424985
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00439112289433923
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324484566243138
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168556985024252
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00584396513888457
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107737864286784
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00393715385870072
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123507592128815
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000760934589088901
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.0072373918784976
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00310402087257472
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00166055638008123
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0248004772423482
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00645960857760528
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00617725409521416
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00249568240113506
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00619106773212341

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.