Coexpression cluster:C3973

Full id: C3973_bronchogenic_chorionic_hepatoblastoma_small_testicular_rectum_adenocarcinoma

Phase1 CAGE Peaks

Hg19::chr1:3371210..3371219,+	p9@ARHGEF16
Hg19::chr1:3371222..3371243,+	p1@ARHGEF16
Hg19::chr1:3371261..3371278,+	p4@ARHGEF16

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	1.55e-33	253
endodermal cell	2.53e-14	58
endo-epithelial cell	3.49e-14	42
epithelial cell of alimentary canal	1.91e-08	20
kidney tubule cell	1.70e-07	10
nephron tubule epithelial cell	1.70e-07	10
germ line cell	1.89e-07	7
germ cell	1.89e-07	7
embryonic stem cell	5.78e-07	5
epithelial cell of lung	6.60e-07	19
respiratory epithelial cell	9.21e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	2.23e-21	160
endoderm	2.23e-21	160
presumptive endoderm	2.23e-21	160
digestive system	3.17e-19	145
digestive tract	3.17e-19	145
primitive gut	3.17e-19	145
subdivision of digestive tract	1.28e-18	118
trunk region element	5.78e-13	101
respiratory primordium	1.79e-12	38
endoderm of foregut	1.79e-12	38
respiratory tract	1.79e-12	54
foregut	1.80e-12	87
respiratory system	1.06e-11	74
segment of respiratory tract	3.04e-11	47
urinary system structure	1.33e-09	47
renal system	3.25e-09	48
subdivision of trunk	4.31e-09	112
gastrointestinal system	5.25e-09	25
organ system subdivision	9.42e-09	223
immaterial anatomical entity	1.15e-08	117
larynx	1.16e-08	9
organ part	1.34e-08	218
endo-epithelium	3.16e-08	82
anatomical space	3.28e-08	95
cavitated compound organ	5.17e-08	31
organ segment	6.92e-08	98
kidney	1.02e-07	26
kidney mesenchyme	1.02e-07	26
upper urinary tract	1.02e-07	26
kidney rudiment	1.02e-07	26
kidney field	1.02e-07	26
organ	1.25e-07	503
nephron tubule epithelium	1.70e-07	10
abdomen element	4.05e-07	54
abdominal segment element	4.05e-07	54
respiratory tract epithelium	6.60e-07	19
lung epithelium	6.60e-07	19

Disease

Ontology term	p-value	n
carcinoma	2.84e-41	106
cell type cancer	1.56e-29	143
cancer	2.25e-16	235
disease of cellular proliferation	8.09e-16	239
squamous cell carcinoma	1.03e-09	14
adenocarcinoma	3.98e-08	25

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	0.0279709254124962
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171929344348622
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032567605818757
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322585811271754
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320953450022959
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00664591910148469
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309336835228226
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190479579918148
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421993484773737
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140359582220808
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109525123020795

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.