Coexpression cluster:C1532

Full id: C1532_CD14_serous_clear_pharyngeal_epidermoid_large_glassy

Phase1 CAGE Peaks

Hg19::chr6:126240356..126240379,+	p7@NCOA7
Hg19::chr6:126240380..126240430,+	p2@NCOA7
Hg19::chr6:126240442..126240459,+	p4@NCOA7
Hg19::chr6:126240463..126240489,+	p6@NCOA7
Hg19::chr6:126240490..126240501,+	p11@NCOA7
Hg19::chr6:126240542..126240553,+	p14@NCOA7

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
classical monocyte	2.14e-09	45
CD14-positive, CD16-negative classical monocyte	3.99e-08	42
endodermal cell	5.98e-07	59

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	1.48e-15	169
endoderm	1.48e-15	169
presumptive endoderm	1.48e-15	169
digestive system	2.21e-14	155
digestive tract	2.21e-14	155
primitive gut	2.21e-14	155
subdivision of digestive tract	4.94e-14	129
endodermal part of digestive tract	4.94e-14	129
mixed endoderm/mesoderm-derived structure	7.75e-12	130
foregut	1.28e-10	98
mesoderm	2.74e-10	448
mesoderm-derived structure	2.74e-10	448
presumptive mesoderm	2.74e-10	448
respiratory system	1.18e-07	72
larynx	3.91e-07	9
primordium	5.36e-07	168

Disease

Ontology term	p-value	n
carcinoma	4.35e-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
BCLAF1#9774	6	21.6526476101218	9.68736949628703e-09	7.35275568911861e-07
CEBPB#1051	6	7.97114762582482	3.89609159898068e-06	0.000127078048252949
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.00205354839872016
ELK4#2005	6	16.235681658468	5.45305335722442e-08	3.44532026361259e-06
EP300#2033	6	6.7739417262232	1.03454107484288e-05	0.000269981097739919
FOXA1#3169	6	11.0814197493855	5.39600313513231e-07	2.50914145783652e-05
FOXA2#3170	6	24.6304637526652	4.47024549595265e-09	3.61913154536278e-07
HDAC2#3066	6	13.4156202366263	1.71355402088576e-07	9.4339414015439e-06
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00253486039907074
HNF4A#3172	6	23.1322903629537	6.51490260560877e-09	5.14293207276776e-07
HNF4G#3174	6	28.7534225264468	1.76556713337063e-09	1.54304657608448e-07
MAX#4149	6	6.45255550900712	1.3848964723355e-05	0.00033465340739067
MEF2A#4205	6	18.7432309096441	2.30307332780908e-08	1.62961162115889e-06
NFKB1#4790	6	5.48806342419384	3.65870229532191e-05	0.00070787552615992
PAX5#5079	6	6.66956553117783	1.13557256338955e-05	0.000290041728901543
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380731342664033
PRDM1#639	6	131.830955777461	1.88485626211077e-13	2.86539305907695e-11
SIN3A#25942	6	5.40888472681514	3.99207083571449e-05	0.00074345200786588
SP1#6667	6	5.6983813781409	2.91961319085282e-05	0.00060996495707037
SRF#6722	6	13.7971782621678	1.44812893459755e-07	8.1796180530251e-06
STAT1#6772	6	20.7065874971992	1.2666425711927e-08	9.3953752480678e-07
STAT2#6773	6	65.2637711864407	1.28736137622248e-11	1.59490788578054e-09
STAT3#6774	6	10.5194649971542	7.37398960627247e-07	3.27020000207852e-05
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573783578900867
TBP#6908	6	3.70677068709639	0.00038541647290796	0.0037813537824363
TCF7L2#6934	6	10.7701765631373	6.40204410218762e-07	2.91466034868515e-05
TRIM28#10155	6	18.5905250452625	2.41896703530258e-08	1.697812487903e-06

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.