Coexpression cluster:C860

Full id: C860_serous_mesothelioma_Renal_clear_colon_endometrial_hepatoblastoma

Phase1 CAGE Peaks

Hg19::chr6:24178711..24178718,-	p@chr6:24178711..24178718 -
Hg19::chr6:24178792..24178829,+	p@chr6:24178792..24178829 +
Hg19::chr6:24278432..24278446,-	p@chr6:24278432..24278446 -
Hg19::chr6:24345366..24345371,-	p@chr6:24345366..24345371 -
Hg19::chr6:24358088..24358099,-	p5@DCDC2
Hg19::chr6:24358114..24358125,-	p4@DCDC2
Hg19::chr6:24358146..24358176,-	p1@DCDC2
Hg19::chr6:24358196..24358199,-	p8@DCDC2
Hg19::chr6:24358226..24358239,-	p3@DCDC2
Hg19::chr6:24358264..24358295,-	p2@DCDC2

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
kidney cell	1.93e-11	18
kidney epithelial cell	1.93e-11	18
epithelial cell of nephron	7.30e-10	16
kidney tubule cell	8.03e-09	12
nephron tubule epithelial cell	8.03e-09	12
epithelial cell	5.12e-08	254
kidney cortical cell	3.52e-07	13
renal cortical epithelial cell	3.52e-07	13

Uber Anatomy

Ontology term	p-value	n
immaterial anatomical entity	3.48e-14	126
abdomen element	5.11e-14	55
abdominal segment element	5.11e-14	55
multi-tissue structure	8.17e-14	347
neurectoderm	1.09e-13	90
kidney	2.04e-13	27
kidney mesenchyme	2.04e-13	27
kidney rudiment	2.04e-13	27
kidney field	2.04e-13	27
organ	4.34e-13	511
cavitated compound organ	5.27e-13	32
neural plate	1.60e-12	86
presumptive neural plate	1.60e-12	86
urinary system structure	3.46e-12	44
anatomical cavity	4.28e-12	70
intermediate mesoderm	5.57e-12	37
gut epithelium	8.86e-12	54
renal system	1.12e-11	45
body cavity precursor	1.53e-11	63
trunk region element	1.81e-11	107
mesonephros	2.18e-11	18
pronephros	2.18e-11	18
nephrogenic cord	2.18e-11	18
pronephric mesoderm	2.18e-11	18
rostral part of nephrogenic cord	2.18e-11	18
presumptive pronephric mesoderm	2.18e-11	18
abdominal segment of trunk	2.26e-11	61
abdomen	2.26e-11	61
anatomical space	2.50e-11	104
adult organism	2.70e-11	115
reproductive structure	2.87e-11	59
reproductive system	2.87e-11	59
urogenital ridge	7.52e-11	20
excretory tube	9.79e-11	17
mesonephric epithelium	9.79e-11	17
mesonephric tubule	9.79e-11	17
nephric duct	9.79e-11	17
kidney epithelium	9.79e-11	17
renal duct	9.79e-11	17
mesonephric duct	9.79e-11	17
pronephric duct	9.79e-11	17
endo-epithelium	1.35e-10	82
duct	1.78e-10	26
nephron epithelium	7.30e-10	16
nephron	7.30e-10	16
uriniferous tubule	7.30e-10	16
metanephric mesenchyme	7.30e-10	16
nephrogenic mesenchyme	7.30e-10	16
pre-chordal neural plate	1.39e-09	61
epithelium	1.83e-09	309
reproductive organ	1.98e-09	48
organism subdivision	2.75e-09	365
cell layer	4.39e-09	312
intraembryonic coelom	6.20e-09	21
primordium	6.42e-09	168
subdivision of trunk	6.74e-09	113
renal tubule	8.03e-09	12
nephron tubule	8.03e-09	12
nephron tubule epithelium	8.03e-09	12
pigment epithelium of eye	1.41e-08	11
regional part of nervous system	1.49e-08	94
nervous system	1.49e-08	94
anterior region of body	4.39e-08	129
craniocervical region	4.39e-08	129
cortex	8.53e-08	16
digestive system	9.03e-08	155
digestive tract	9.03e-08	155
primitive gut	9.03e-08	155
neural tube	1.05e-07	57
neural rod	1.05e-07	57
future spinal cord	1.05e-07	57
neural keel	1.05e-07	57
ectoderm	1.13e-07	173
presumptive ectoderm	1.13e-07	173
embryo	1.28e-07	612
male organism	1.56e-07	22
male reproductive system	1.56e-07	22
gonad	1.84e-07	21
indifferent external genitalia	1.84e-07	21
indifferent gonad	1.84e-07	21
gonad primordium	1.84e-07	21
head	1.86e-07	123
organ part	1.90e-07	219
regional part of brain	2.91e-07	59
cortex of kidney	3.52e-07	13
renal parenchyma	3.52e-07	13
embryonic structure	5.78e-07	605
developing anatomical structure	5.78e-07	605
external genitalia	6.69e-07	22
ectoderm-derived structure	6.75e-07	169
subdivision of digestive tract	8.56e-07	129

Disease

Ontology term	p-value	n

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	6	4.78268857549489	0.000520075535673016	0.0045060700904392
CTCF#10664	6	3.21615382384502	0.00442909532615486	0.0209706359039028
GABPB1#2553	6	4.2406103017093	0.00100657891610646	0.00721177851541763
HDAC2#3066	6	8.04937214197576	2.76518202234458e-05	0.000584719265502421
MYC#4609	6	3.13336912296564	0.00507742326845552	0.0236310609952864
TCF7L2#6934	6	6.46210593788241	9.65893777244962e-05	0.00137509514996846

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.