Coexpression cluster:C572

Full id: C572_Urothelial_Prostate_Keratinocyte_Corneal_Mammary_Bronchial_Gingival

Phase1 CAGE Peaks

Hg19::chr2:20401847..20401864,-	p@chr2:20401847..20401864 -
Hg19::chr2:20402086..20402095,-	p@chr2:20402086..20402095 -
Hg19::chr2:20402138..20402149,-	p@chr2:20402138..20402149 -
Hg19::chr2:20402306..20402318,-	p@chr2:20402306..20402318 -
Hg19::chr2:20402607..20402620,-	p@chr2:20402607..20402620 -
Hg19::chr2:20402634..20402650,-	p@chr2:20402634..20402650 -
Hg19::chr2:20402663..20402684,-	p@chr2:20402663..20402684 -
Hg19::chr2:20403746..20403774,+	p@chr2:20403746..20403774 +
Hg19::chr2:20404043..20404055,-	p@chr2:20404043..20404055 -
Hg19::chr2:20405127..20405142,-	p@chr2:20405127..20405142 -
Hg19::chr2:20424816..20424834,-	p1@SDC1
Hg19::chr2:20424844..20424863,-	p2@SDC1
Hg19::chr2:20424884..20424897,-	p3@SDC1
Hg19::chr2:20425105..20425154,-	p7@SDC1
Hg19::chr2:20425158..20425206,-	p6@SDC1
Hg19::chr2:20425208..20425273,-	p5@SDC1

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	6.58e-35	254
embryonic cell	2.98e-19	248
endodermal cell	1.28e-17	59
endo-epithelial cell	5.34e-17	43
respiratory epithelial cell	6.57e-09	13
ectodermal cell	7.51e-08	71
epithelial cell of alimentary canal	4.90e-07	21

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	1.21e-28	169
endoderm	1.21e-28	169
presumptive endoderm	1.21e-28	169
mesenchyme	1.83e-22	238
entire embryonic mesenchyme	1.83e-22	238
digestive system	2.78e-22	155
digestive tract	2.78e-22	155
primitive gut	2.78e-22	155
organism subdivision	2.00e-20	365
mixed endoderm/mesoderm-derived structure	1.50e-19	130
subdivision of digestive tract	7.16e-19	129
endodermal part of digestive tract	7.16e-19	129
trunk	2.57e-18	216
multi-tissue structure	1.10e-17	347
immaterial anatomical entity	3.97e-17	126
anatomical space	1.01e-14	104
respiratory system	5.10e-14	72
trunk region element	9.08e-14	107
surface structure	9.74e-14	95
foregut	1.00e-13	98
subdivision of trunk	1.39e-13	113
endo-epithelium	4.62e-13	82
primordium	3.38e-12	168
multi-cellular organism	4.71e-12	659
respiratory tract	1.02e-10	53
anatomical group	1.44e-10	626
epithelial bud	2.21e-10	37
renal system	2.30e-10	45
trunk mesenchyme	2.47e-10	143
anatomical system	2.60e-10	625
urinary system structure	3.86e-10	44
organ	8.23e-10	511
thoracic cavity element	1.12e-09	34
thoracic cavity	1.12e-09	34
orifice	1.55e-09	35
organ part	2.79e-09	219
respiratory primordium	4.59e-09	38
endoderm of foregut	4.59e-09	38
reproductive structure	6.64e-09	59
reproductive system	6.64e-09	59
female organism	7.51e-09	41
thoracic segment organ	7.89e-09	35
epithelial fold	1.32e-08	51
embryo	1.65e-08	612
segment of respiratory tract	5.70e-08	46
subdivision of head	9.15e-08	48
embryonic structure	9.90e-08	605
developing anatomical structure	9.90e-08	605
thoracic segment of trunk	1.13e-07	52
abdomen element	1.30e-07	55
abdominal segment element	1.30e-07	55
intermediate mesoderm	1.59e-07	37
germ layer	1.67e-07	604
embryonic tissue	1.67e-07	604
presumptive structure	1.67e-07	604
epiblast (generic)	1.67e-07	604
cell layer	3.21e-07	312
tracheobronchial tree	3.81e-07	14
lower respiratory tract	3.81e-07	14
female reproductive organ	5.16e-07	37
female reproductive system	5.16e-07	37
anatomical cavity	5.56e-07	70
reproductive organ	6.43e-07	48
abdominal segment of trunk	7.20e-07	61
abdomen	7.20e-07	61
exocrine gland	7.20e-07	31
exocrine system	7.20e-07	31
internal genitalia	7.26e-07	25
epithelium	9.71e-07	309

Disease

Ontology term	p-value	n
carcinoma	4.40e-15	106
cell type cancer	6.16e-13	143
squamous cell carcinoma	7.00e-07	14

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
CTCFL#140690	5	6.17077323717949	0.000907547910546213	0.00660741695570136
HDAC2#3066	6	5.03085758873485	0.000712452802920075	0.00572500256091172
RAD21#5885	6	3.88313771079612	0.00275811930147602	0.015123390650856
RXRA#6256	6	7.52798142717498	7.91408951389162e-05	0.00121229040003128
SMC3#9126	6	5.64184981684982	0.000385101594797398	0.00377932958645419
ZNF143#7702	6	5.06282870708546	0.000688795891547956	0.00555327729792936

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.