Coexpression cluster:C885

Full id: C885_breast_Intestinal_MCF7_Prostate_small_colon_Hepatocyte

Phase1 CAGE Peaks

Hg19::chr11:72493722..72493753,-	p9@STARD10
Hg19::chr14:38060540..38060566,-	p@chr14:38060540..38060566 -
Hg19::chr14:38061906..38061927,-	p@chr14:38061906..38061927 -
Hg19::chr14:38064495..38064506,-	p4@FOXA1
Hg19::chr14:38064536..38064550,-	p7@FOXA1
Hg19::chr14:38064554..38064559,-	p12@FOXA1
Hg19::chr14:38064572..38064584,-	p5@FOXA1
Hg19::chr14:38064590..38064606,-	p2@FOXA1
Hg19::chr14:38064797..38064843,+	p1@TTC6

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:0042593	glucose homeostasis	0.0231308033864625
GO:0033500	carbohydrate homeostasis	0.0231308033864625
GO:0048754	branching morphogenesis of a tube	0.0231308033864625
GO:0001763	morphogenesis of a branching structure	0.0231308033864625
GO:0030855	epithelial cell differentiation	0.0231308033864625
GO:0030324	lung development	0.0231308033864625
GO:0030323	respiratory tube development	0.0231308033864625
GO:0002009	morphogenesis of an epithelium	0.029644417655839
GO:0035239	tube morphogenesis	0.033114259988823
GO:0042445	hormone metabolic process	0.033114259988823
GO:0035295	tube development	0.0400073614017467
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0435551382564899

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	6.34e-19	253
endodermal cell	5.06e-10	58
metabolising cell	3.64e-08	12
endopolyploid cell	3.64e-08	12
parenchymal cell	3.64e-08	12
polyploid cell	3.64e-08	12
hepatocyte	3.64e-08	12
epithelial cell of prostate	8.09e-07	3

Uber Anatomy

Ontology term	p-value	n
subdivision of digestive tract	6.49e-34	118
digestive system	3.14e-31	145
digestive tract	3.14e-31	145
primitive gut	3.14e-31	145
endoderm-derived structure	6.35e-28	160
endoderm	6.35e-28	160
presumptive endoderm	6.35e-28	160
endo-epithelium	1.61e-21	82
foregut	3.20e-20	87
subdivision of trunk	4.48e-16	112
epithelium of foregut-midgut junction	1.80e-15	25
anatomical boundary	1.80e-15	25
hepatobiliary system	1.80e-15	25
foregut-midgut junction	1.80e-15	25
septum transversum	1.80e-15	25
trunk region element	1.11e-14	101
gut epithelium	1.50e-14	54
epithelial bud	9.15e-14	37
sac	6.96e-13	26
digestive tract diverticulum	7.17e-13	23
organ system subdivision	7.95e-13	223
respiratory primordium	1.73e-12	38
endoderm of foregut	1.73e-12	38
trunk	3.55e-12	199
epithelial sac	1.23e-11	25
hepatic diverticulum	1.41e-11	22
liver primordium	1.41e-11	22
respiratory tract	1.53e-10	54
organism subdivision	1.97e-10	264
immaterial anatomical entity	7.18e-10	117
epithelial fold	8.58e-10	47
thoracic segment of trunk	8.94e-10	52
respiratory system	9.88e-10	74
multi-tissue structure	2.05e-09	342
lung	3.77e-09	22
respiratory tube	3.77e-09	22
respiration organ	3.77e-09	22
pair of lungs	3.77e-09	22
lung primordium	3.77e-09	22
lung bud	3.77e-09	22
gland	5.47e-09	59
hindgut	9.08e-09	19
abdomen element	1.30e-08	54
abdominal segment element	1.30e-08	54
thoracic cavity element	1.49e-08	34
thoracic cavity	1.49e-08	34
thoracic segment organ	3.27e-08	35
cloaca	6.09e-08	14
anal region	6.09e-08	14
embryonic cloaca	6.09e-08	14
terminal part of digestive tract	6.09e-08	14
primitive urogenital sinus	6.09e-08	14
proctodeum	6.09e-08	14
segment of respiratory tract	7.05e-08	47
intestine	7.53e-08	17
liver	8.12e-08	19
digestive gland	8.12e-08	19
liver bud	8.12e-08	19
biliary system	2.11e-07	9
biliary tree	2.11e-07	9
biliary bud	2.11e-07	9
genitourinary system	2.59e-07	15
gastrointestinal system	2.69e-07	25
abdominal segment of trunk	2.76e-07	60
abdomen	2.76e-07	60

Disease

Ontology term	p-value	n
carcinoma	6.68e-43	106
cell type cancer	1.18e-27	143
cancer	2.82e-15	235
disease of cellular proliferation	1.24e-14	239
disease of anatomical entity	8.56e-13	39
thoracic cancer	4.02e-10	4
breast cancer	4.02e-10	4
squamous cell carcinoma	1.82e-09	14
respiratory system cancer	8.62e-09	16
lung carcinoma	1.06e-07	9
lung cancer	1.20e-07	15

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	6	3.27159280991955	0.00338995924180989	0.0173008186696336
EP300#2033	6	4.51596115081547	0.000579924810993498	0.00486597311282638
FOXA1#3169	6	7.38761316625697	3.56196695095157e-05	0.000689926310071275
FOXA2#3170	6	16.4203091684435	3.37701953018255e-07	1.67789030786268e-05
GATA3#2625	6	18.1576775714707	1.86572751230391e-07	1.01804971607894e-05
HEY1#23462	7	3.14230858908222	0.00125876346284377	0.00845699564464074
HNF4A#3172	5	12.8512724238632	1.64120812799935e-05	0.000378965588503481
MYC#4609	7	4.06177478902954	0.000235555679657337	0.00256743890917686
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.00728442666109421
RXRA#6256	6	13.3830780927555	1.12450168564813e-06	4.62551522439564e-05
SIN3A#25942	6	3.60592315121009	0.00200305799133432	0.0116466637098856
ZBTB7A#51341	6	4.90127287191726	0.000366991098105653	0.00365622276972778

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.