Coexpression cluster:C619

Full id: C619_squamous_bile_Small_Mammary_mucinous_Tracheal_giant

Phase1 CAGE Peaks

Hg19::chr11:128376979..128377025,-	p@chr11:128376979..128377025 -
Hg19::chr12:31910006..31910040,-	p@chr12:31910006..31910040 -
Hg19::chr20:10400351..10400358,-	p@chr20:10400351..10400358 -
Hg19::chr20:10400359..10400384,-	p@chr20:10400359..10400384 -
Hg19::chr20:10400400..10400411,-	p@chr20:10400400..10400411 -
Hg19::chr2:20133179..20133195,-	p@chr2:20133179..20133195 -
Hg19::chr2:20133198..20133223,-	p@chr2:20133198..20133223 -
Hg19::chr2:29353197..29353206,-	p@chr2:29353197..29353206 -
Hg19::chr2:29353207..29353220,-	p@chr2:29353207..29353220 -
Hg19::chr2:29353224..29353251,-	p@chr2:29353224..29353251 -
Hg19::chr3:101957544..101957547,+	p@chr3:101957544..101957547 +
Hg19::chr6:150813975..150813994,+	p@chr6:150813975..150813994 +
Hg19::chr6:150813996..150814008,+	p@chr6:150813996..150814008 +
Hg19::chr7:101917407..101917443,+	p3@CUX1

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	4.35e-44	254
animal cell	3.12e-17	679
eukaryotic cell	3.12e-17	679
endo-epithelial cell	3.63e-17	43
squamous epithelial cell	8.91e-17	62
endodermal cell	1.82e-16	59
embryonic cell	1.37e-10	248
native cell	2.52e-09	722
classical monocyte	2.05e-08	45
respiratory epithelial cell	6.47e-08	13
CD14-positive, CD16-negative classical monocyte	1.03e-07	42
epithelial cell of lung	3.97e-07	19
epithelial cell of alimentary canal	7.16e-07	21

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	5.53e-22	169
endoderm	5.53e-22	169
presumptive endoderm	5.53e-22	169
digestive system	1.26e-18	155
digestive tract	1.26e-18	155
primitive gut	1.26e-18	155
subdivision of digestive tract	2.64e-13	129
endodermal part of digestive tract	2.64e-13	129
mixed endoderm/mesoderm-derived structure	5.97e-13	130
endo-epithelium	2.66e-12	82
respiratory system	4.87e-12	72
respiratory tract	1.74e-11	53
respiratory primordium	7.84e-11	38
endoderm of foregut	7.84e-11	38
organ	1.06e-10	511
epithelial bud	3.51e-10	37
segment of respiratory tract	5.94e-10	46
foregut	6.69e-10	98
anatomical system	1.24e-09	625
anatomical group	1.98e-09	626
trunk region element	7.61e-09	107
multi-cellular organism	3.33e-08	659
thoracic cavity element	4.59e-08	34
thoracic cavity	4.59e-08	34
anatomical space	4.62e-08	104
immaterial anatomical entity	8.11e-08	126
urinary system structure	1.16e-07	44
renal system	1.30e-07	45
epithelial fold	1.82e-07	51
thoracic segment organ	1.95e-07	35
mesenchyme	2.94e-07	238
entire embryonic mesenchyme	2.94e-07	238
respiratory tract epithelium	3.97e-07	19
lung epithelium	3.97e-07	19
mesoderm	4.51e-07	448
mesoderm-derived structure	4.51e-07	448
presumptive mesoderm	4.51e-07	448
respiratory system epithelium	8.63e-07	28

Disease

Ontology term	p-value	n
carcinoma	6.78e-25	106
cell type cancer	1.01e-17	143
disease of cellular proliferation	7.82e-10	239
cancer	1.97e-09	235
adenocarcinoma	5.45e-09	25
squamous cell carcinoma	6.30e-09	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
BCL3#602	3	7.40295060080107	0.00694426632847338	0.0293719516879731
CEBPB#1051	7	3.98557381291241	0.000747204341923996	0.00588338919377264
EP300#2033	10	4.83852980444514	2.76491461776768e-06	9.56808872647577e-05
FOS#2353	6	3.85626656095475	0.00255626107611445	0.0141450328774143
FOSL1#8061	5	14.1834213272761	1.67209788666175e-05	0.00038550161409507
FOSL2#2355	5	6.04650021591489	0.000915800219548301	0.00666424603744461
GATA3#2625	3	5.83639636225843	0.013286841502602	0.0469885019534827
JUN#3725	6	5.36264108242986	0.000444602832349908	0.004139229382046
JUND#3727	10	4.99618852990788	2.04570531488249e-06	7.46771818878058e-05
MAFF#23764	3	12.0675763907025	0.00175844773885572	0.0108074220795829
MAFK#7975	3	5.80729995810641	0.0134669729606905	0.0475723723673787
NFE2#4778	3	16.5437701396348	0.000709930270545248	0.0057051714008522
POLR2A#5430	13	1.99406366394678	0.000384568890376538	0.00377481112237173
STAT3#6774	8	6.01112285551671	1.1795981756812e-05	0.000298801973975184

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.