Coexpression cluster:C2102

Full id: C2102_amniotic_cervical_Placental_chorionic_Hep2_salivary_Corneal

Phase1 CAGE Peaks

Hg19::chr11:119994643..119994655,-	p10@TRIM29
Hg19::chr11:119999506..119999529,-	p7@TRIM29
Hg19::chr11:119999539..119999579,-	p3@TRIM29
Hg19::chr11:119999611..119999625,-	p9@TRIM29

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	1.76e-16	254
endo-epithelial cell	1.06e-14	43
endodermal cell	1.01e-09	59
epithelial cell of alimentary canal	3.01e-09	21
general ecto-epithelial cell	4.96e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	2.15e-18	169
endoderm	2.15e-18	169
presumptive endoderm	2.15e-18	169
respiratory system	6.23e-17	72
digestive system	1.86e-13	155
digestive tract	1.86e-13	155
primitive gut	1.86e-13	155
mixed endoderm/mesoderm-derived structure	1.92e-11	130
organ	2.31e-11	511
subdivision of digestive tract	2.36e-11	129
endodermal part of digestive tract	2.36e-11	129
respiratory tract	4.51e-11	53
orifice	4.87e-11	35
larynx	1.37e-09	9
extraembryonic membrane	3.83e-09	14
membranous layer	3.83e-09	14
respiratory primordium	5.01e-09	38
endoderm of foregut	5.01e-09	38
oral opening	6.23e-09	21
organ part	7.31e-09	219
upper respiratory tract	2.08e-08	19
segment of respiratory tract	3.77e-08	46
foregut	4.27e-08	98
surface structure	2.22e-07	95
chorion	3.31e-07	7

Disease

Ontology term	p-value	n
carcinoma	3.44e-10	106

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
BRCA1#672	3	15.1381729824178	0.000468218442143119	0.00429968046065112
CEBPB#1051	3	5.97836071936861	0.00715383248472697	0.0297155912529293
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418670103910971
FOXA1#3169	3	8.31106481203909	0.00274013818210985	0.0150318989180255
GATA3#2625	3	20.4273872679045	0.000192441557625832	0.00231895740589411
JUN#3725	3	9.38462189425225	0.00191899450203047	0.0112809786557222
MAX#4149	3	4.83941663175534	0.0131573713783684	0.046589005234291
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186190398351055
NR3C1#2908	3	11.2297674983798	0.00113167206806385	0.00775173470955079
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123798267886743
SMARCB1#6598	3	13.6895368358681	0.000630578340937934	0.00517947081000526
SMC3#9126	3	11.2836996336996	0.00111580236686805	0.00765407444291184
STAT1#6772	3	15.5299406228994	0.00043408865517555	0.00404747656975977
STAT3#6774	3	7.88959874786568	0.00319076048168013	0.0167381502810885
TFAP2A#7020	4	16.518634373045	1.34240829060362e-05	0.000325970191728322
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.0011437056552575

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.