Coexpression cluster:C2562

Full id: C2562_Urothelial_Gingival_Keratinocyte_Mammary_Bronchial_Small_Mallassezderived

Phase1 CAGE Peaks

Hg19::chr1:209826369..209826380,-	p@chr1:209826369..209826380 -
Hg19::chr1:209826396..209826431,-	p@chr1:209826396..209826431 -
Hg19::chr1:209826442..209826464,-	p@chr1:209826442..209826464 -
Hg19::chr1:209826486..209826491,-	p@chr1:209826486..209826491 -

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	3.63e-36	254
endo-epithelial cell	5.16e-23	43
endodermal cell	3.81e-18	59
respiratory epithelial cell	2.00e-11	13
epithelial cell of alimentary canal	9.51e-09	21
general ecto-epithelial cell	2.34e-08	13
epithelial cell of tracheobronchial tree	2.75e-08	9
epithelial cell of lower respiratory tract	2.75e-08	9
ecto-epithelial cell	2.21e-07	33

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	2.95e-20	169
endoderm	2.95e-20	169
presumptive endoderm	2.95e-20	169
digestive system	2.07e-14	155
digestive tract	2.07e-14	155
primitive gut	2.07e-14	155
subdivision of digestive tract	4.24e-13	129
endodermal part of digestive tract	4.24e-13	129
respiratory system	1.15e-12	72
mixed endoderm/mesoderm-derived structure	3.56e-12	130
respiratory tract	1.37e-11	53
respiratory primordium	3.43e-10	38
endoderm of foregut	3.43e-10	38
organ	9.65e-10	511
anatomical space	1.15e-08	104
endo-epithelium	1.36e-08	82
foregut	1.41e-08	98
urinary system structure	1.67e-08	44
segment of respiratory tract	2.46e-08	46
epithelial bud	3.30e-08	37
renal system	4.42e-08	45
immaterial anatomical entity	1.78e-07	126
extraembryonic membrane	2.93e-07	14
membranous layer	2.93e-07	14
trunk region element	4.57e-07	107
reproductive structure	6.98e-07	59
reproductive system	6.98e-07	59

Disease

Ontology term	p-value	n
carcinoma	1.72e-21	106
cell type cancer	1.53e-15	143
adenocarcinoma	1.47e-08	25
squamous cell carcinoma	2.01e-08	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
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106541521290241
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00434487817847948
ESR1#2099	4	30.7686032961545	1.11467714392546e-06	4.610525395423e-05
JUN#3725	4	12.5128291923363	4.07770316866756e-05	0.00074362011739562
JUNB#3726	4	30.6106326598211	1.13787152942193e-06	4.66032018279597e-05
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00391901195083592
REST#5978	4	9.65002871612802	0.000115282561421917	0.00157139068550556
SMARCB1#6598	4	18.2527157811574	9.00423392720929e-06	0.000241746320597381
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.00043817813892143
STAT3#6774	4	10.5194649971542	8.16377768286615e-05	0.00123192714552934
TFAP2A#7020	4	16.518634373045	1.34240829060362e-05	0.000326653726613121
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114593343073223

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.