Coexpression cluster:C326

Full id: C326_bile_choriocarcinoma_giant_lung_mucinous_glassy_malignant

Phase1 CAGE Peaks

Hg19::chr10:128112935..128112946,+	p@chr10:128112935..128112946 +
Hg19::chr10:5075825..5075836,+	p@chr10:5075825..5075836 +
Hg19::chr10:5075837..5075848,+	p@chr10:5075837..5075848 +
Hg19::chr11:110129024..110129031,-	p19@RDX
Hg19::chr11:110129088..110129096,-	p18@RDX
Hg19::chr11:41899631..41899640,-	p@chr11:41899631..41899640 -
Hg19::chr12:132340327..132340336,+	p@chr12:132340327..132340336 +
Hg19::chr12:15815672..15815681,-	p27@EPS8
Hg19::chr12:15815704..15815714,-	p24@EPS8
Hg19::chr12:19842219..19842224,+	p@chr12:19842219..19842224 +
Hg19::chr12:19842253..19842299,+	p@chr12:19842253..19842299 +
Hg19::chr12:19842421..19842428,+	p@chr12:19842421..19842428 +
Hg19::chr12:19842430..19842437,+	p@chr12:19842430..19842437 +
Hg19::chr12:19842439..19842446,+	p@chr12:19842439..19842446 +
Hg19::chr14:32476072..32476090,+	p1@ENST00000556949
Hg19::chr15:75682218..75682225,-	p@chr15:75682218..75682225 -
Hg19::chr15:75682252..75682263,-	p@chr15:75682252..75682263 -
Hg19::chr15:89659033..89659044,+	p@chr15:89659033..89659044 +
Hg19::chr17:77809975..77809980,-	p@chr17:77809975..77809980 -
Hg19::chr19:16023475..16023478,-	p@chr19:16023475..16023478 -
Hg19::chr1:164600166..164600175,+	p47@PBX1
Hg19::chr1:164600184..164600191,+	p38@PBX1
Hg19::chr1:197964894..197964906,-	p@chr1:197964894..197964906 -
Hg19::chr1:241804444..241804477,-	p@chr1:241804444..241804477 -
Hg19::chr2:239198771..239198784,-	p7@PER2
Hg19::chr3:192362159..192362169,-	p@chr3:192362159..192362169 -
Hg19::chr4:178243549..178243558,+	p@chr4:178243549..178243558 +
Hg19::chr5:66178685..66178698,+	p@chr5:66178685..66178698 +
Hg19::chr5:66178707..66178713,+	p@chr5:66178707..66178713 +
Hg19::chr6:79960170..79960171,-	p@chr6:79960170..79960171 -
Hg19::chr7:128543063..128543091,-	p@chr7:128543063..128543091 -
Hg19::chr7:143953304..143953314,-	p1@uc003wed.2
Hg19::chr7:143953331..143953349,-	p1@OR2A20P
Hg19::chr7:389967..389980,+	p@chr7:389967..389980 +
Hg19::chr9:131397542..131397587,-	p@chr9:131397542..131397587 -

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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GO ID	GO name	FDR corrected p-value
GO:0030033	microvillus biogenesis	0.0173045506176316
GO:0032528	microvillus organization and biogenesis	0.0173045506176316
GO:0051123	transcriptional preinitiation complex assembly	0.0173045506176316
GO:0045898	regulation of transcriptional preinitiation complex assembly	0.0173045506176316
GO:0032420	stereocilium	0.0173045506176316
GO:0032421	stereocilium bundle	0.0173045506176316
GO:0045176	apical protein localization	0.0188726906492033
GO:0030175	filopodium	0.0188726906492033
GO:0008105	asymmetric protein localization	0.0188726906492033
GO:0007016	cytoskeletal anchoring	0.0188726906492033
GO:0006700	C21-steroid hormone biosynthetic process	0.0188726906492033
GO:0008207	C21-steroid hormone metabolic process	0.0198852996184453
GO:0005902	microvillus	0.0198852996184453
GO:0051693	actin filament capping	0.0198852996184453
GO:0007530	sex determination	0.0198852996184453
GO:0051016	barbed-end actin filament capping	0.0198852996184453
GO:0030835	negative regulation of actin filament depolymerization	0.0198852996184453
GO:0030902	hindbrain development	0.0198852996184453
GO:0030834	regulation of actin filament depolymerization	0.0198852996184453
GO:0030042	actin filament depolymerization	0.0198852996184453
GO:0007623	circadian rhythm	0.023872501376074
GO:0007173	epidermal growth factor receptor signaling pathway	0.0259258954015117
GO:0030027	lamellipodium	0.0261884710132444
GO:0005515	protein binding	0.0261884710132444
GO:0042446	hormone biosynthetic process	0.0261884710132444
GO:0001726	ruffle	0.0261884710132444
GO:0008064	regulation of actin polymerization and/or depolymerization	0.0261884710132444
GO:0051261	protein depolymerization	0.0261884710132444
GO:0030832	regulation of actin filament length	0.0261884710132444
GO:0032535	regulation of cellular component size	0.0261884710132444
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.0261884710132444
GO:0005070	SH3/SH2 adaptor activity	0.0264473229556302
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0270318444045401
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.0270318444045401
GO:0033043	regulation of organelle organization and biogenesis	0.0270318444045401
GO:0019222	regulation of metabolic process	0.0270318444045401
GO:0060090	molecular adaptor activity	0.0277109664806096
GO:0008154	actin polymerization and/or depolymerization	0.0277109664806096
GO:0031252	leading edge	0.0318538779589705
GO:0045177	apical part of cell	0.0356548518296873
GO:0003006	reproductive developmental process	0.0356548518296873
GO:0042445	hormone metabolic process	0.0356548518296873
GO:0006694	steroid biosynthetic process	0.0356548518296873
GO:0030674	protein binding, bridging	0.0356548518296873
GO:0051128	regulation of cellular component organization and biogenesis	0.0382952347115228
GO:0051248	negative regulation of protein metabolic process	0.0389543544901542
GO:0019898	extrinsic to membrane	0.0392201151579407
GO:0050954	sensory perception of mechanical stimulus	0.0463576165769469
GO:0007605	sensory perception of sound	0.0463576165769469
GO:0007420	brain development	0.0476834017488412
GO:0050794	regulation of cellular process	0.0476834017488412

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	7.14e-11	254
endodermal cell	9.92e-11	59
endo-epithelial cell	8.73e-09	43

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	5.23e-16	169
endoderm	5.23e-16	169
presumptive endoderm	5.23e-16	169
digestive system	2.98e-15	155
digestive tract	2.98e-15	155
primitive gut	2.98e-15	155
subdivision of digestive tract	3.27e-14	129
endodermal part of digestive tract	3.27e-14	129
mixed endoderm/mesoderm-derived structure	1.04e-13	130
foregut	2.25e-13	98
respiratory system	2.41e-11	72
respiratory tract	2.68e-11	53
respiratory primordium	3.34e-10	38
endoderm of foregut	3.34e-10	38
segment of respiratory tract	1.60e-08	46
endo-epithelium	5.21e-08	82

Disease

Ontology term	p-value	n
carcinoma	2.22e-28	106
cell type cancer	3.22e-25	143
disease of cellular proliferation	4.71e-18	239
cancer	5.37e-18	235
adenocarcinoma	1.62e-10	25
squamous cell carcinoma	9.79e-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
CEBPB#1051	15	3.41620612535349	8.07454372054656e-06	0.000224281189263341
EP300#2033	14	2.70957669048928	0.000246950741995258	0.00268491448503464
FOS#2353	11	2.82792881136681	0.00103839505617017	0.00734350902433348
JUN#3725	13	4.64762227143921	1.47511420509808e-06	5.69325397140569e-05
JUND#3727	14	2.79786557674841	0.000174826593741349	0.00212681591424027
NR3C1#2908	10	4.27800666604944	6.83167969732869e-05	0.00109030225536264
POLR3A#11128	2	19.3789777195282	0.0048416696654612	0.0226915786300082
STAT3#6774	12	3.60667371331003	5.5685080397802e-05	0.000940746378464257

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.