Coexpression cluster:C2638

Full id: C2638_breast_bronchogenic_Amniotic_liver_endometrioid_Hepatocyte_serous

Phase1 CAGE Peaks

Hg19::chr22:19950047..19950056,+	p9@COMT
Hg19::chr22:19950060..19950096,+	p3@COMT
Hg19::chr22:19950097..19950117,+	p5@COMT
Hg19::chr22:19950126..19950137,+	p14@COMT

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	9.59e-26	254
endodermal cell	1.48e-14	59
endo-epithelial cell	1.72e-13	43
embryonic cell	1.16e-10	248
epithelial cell of alimentary canal	1.09e-07	21

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	9.05e-20	659
organism subdivision	2.35e-19	365
multi-tissue structure	3.28e-19	347
endoderm-derived structure	1.12e-18	169
endoderm	1.12e-18	169
presumptive endoderm	1.12e-18	169
anatomical conduit	3.90e-18	241
anatomical cluster	1.88e-15	286
anatomical system	2.79e-15	625
embryo	3.41e-15	612
anatomical group	6.09e-15	626
digestive system	8.54e-15	155
digestive tract	8.54e-15	155
primitive gut	8.54e-15	155
epithelium	2.19e-14	309
cell layer	6.38e-14	312
embryonic structure	3.73e-13	605
developing anatomical structure	3.73e-13	605
germ layer	7.04e-13	604
embryonic tissue	7.04e-13	604
presumptive structure	7.04e-13	604
epiblast (generic)	7.04e-13	604
organ part	1.98e-12	219
immaterial anatomical entity	1.04e-11	126
subdivision of digestive tract	2.65e-11	129
endodermal part of digestive tract	2.65e-11	129
organ	5.07e-11	511
mixed endoderm/mesoderm-derived structure	6.86e-11	130
mesenchyme	7.03e-11	238
entire embryonic mesenchyme	7.03e-11	238
trunk	7.60e-11	216
tube	2.68e-10	194
subdivision of trunk	3.08e-10	113
trunk region element	3.11e-09	107
anatomical space	4.35e-09	104
endo-epithelium	6.08e-09	82
respiratory system	6.17e-09	72
orifice	2.62e-08	35
oral opening	6.28e-08	21
head	6.32e-08	123
anterior region of body	1.11e-07	129
craniocervical region	1.11e-07	129
ectoderm-derived structure	1.21e-07	169
thoracic segment of trunk	1.86e-07	52
ectoderm	1.87e-07	173
presumptive ectoderm	1.87e-07	173
trunk mesenchyme	2.00e-07	143
mouth	2.73e-07	28
stomodeum	2.73e-07	28
exocrine gland	3.43e-07	31
exocrine system	3.43e-07	31
foregut	4.31e-07	98
thoracic cavity element	4.65e-07	34
thoracic cavity	4.65e-07	34
extraembryonic membrane	4.70e-07	14
membranous layer	4.70e-07	14
subdivision of head	5.35e-07	48

Disease

Ontology term	p-value	n
squamous cell carcinoma	3.46e-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
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00818022456919604
EBF1#1879	4	8.906466846569	0.0001588790747201	0.00199749267902884
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161049426366166
HDAC2#3066	4	13.4156202366263	3.0859005065161e-05	0.000627020161478667
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186303726294391
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00248299059407042
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00307823661124878
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00888484552163583
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00129540833472911
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.000438461016996911
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00684797327380318
SP2#6668	3	19.6151478703835	0.000217100426924534	0.00248697504525297
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322645533825539
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00249262657650383

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.