Coexpression cluster:C285

Full id: C285_cervical_Hep2_small_colon_temporal_duodenum_bronchogenic

Phase1 CAGE Peaks

Hg19::chr10:99550654..99550658,-	p@chr10:99550654..99550658 -
Hg19::chr11:72957611..72957646,+	p@chr11:72957611..72957646 +
Hg19::chr13:114748246..114748260,-	p@chr13:114748246..114748260 -
Hg19::chr16:15596148..15596153,+	p7@C16orf45
Hg19::chr17:78152310..78152314,+	p10@CARD14
Hg19::chr17:78152323..78152332,+	p3@CARD14
Hg19::chr18:33766737..33766750,-	p@chr18:33766737..33766750 -
Hg19::chr18:5521372..5521391,-	p@chr18:5521372..5521391 -
Hg19::chr1:15850650..15850657,-	p9@CASP9
Hg19::chr1:197411581..197411608,+	p@chr1:197411581..197411608 +
Hg19::chr1:207326648..207326670,+	p@chr1:207326648..207326670 +
Hg19::chr2:233320827..233320853,+	p2@ALPI
Hg19::chr2:233320855..233320886,+	p1@ALPI
Hg19::chr2:233323059..233323070,+	p@chr2:233323059..233323070 +
Hg19::chr2:233324192..233324197,+	p@chr2:233324192..233324197 +
Hg19::chr2:234296792..234296806,+	p13@DGKD
Hg19::chr2:933319..933328,-	p@chr2:933319..933328 -
Hg19::chr2:933356..933367,-	p@chr2:933356..933367 -
Hg19::chr4:173883976..173883983,+	p@chr4:173883976..173883983 +
Hg19::chr4:173883984..173884005,+	p@chr4:173883984..173884005 +
Hg19::chr4:173884006..173884018,+	p@chr4:173884006..173884018 +
Hg19::chr4:173884019..173884038,+	p@chr4:173884019..173884038 +
Hg19::chr4:173884042..173884047,+	p@chr4:173884042..173884047 +
Hg19::chr5:370139..370155,+	p@chr5:370139..370155 +
Hg19::chr5:370156..370169,+	p@chr5:370156..370169 +
Hg19::chr5:37249149..37249162,+	p@chr5:37249149..37249162 +
Hg19::chr5:58571500..58571517,-	p1@uc003jsd.1
Hg19::chr6:1111683..1111701,+	p@chr6:1111683..1111701 +
Hg19::chr6:134664463..134664474,+	p@chr6:134664463..134664474 +
Hg19::chr6:134718844..134718848,+	p@chr6:134718844..134718848 +
Hg19::chr6:152084749..152084760,+	p@chr6:152084749..152084760 +
Hg19::chr6:152084846..152084856,+	p@chr6:152084846..152084856 +
Hg19::chr6:152084870..152084873,+	p@chr6:152084870..152084873 +
Hg19::chr6:152084876..152084885,+	p@chr6:152084876..152084885 +
Hg19::chr6:152084890..152084896,+	p@chr6:152084890..152084896 +
Hg19::chr6:64276121..64276143,-	p@chr6:64276121..64276143 -
Hg19::chr6:64276192..64276203,-	p@chr6:64276192..64276203 -
Hg19::chr6:87797935..87797943,-	p2@CGA
Hg19::chr8:80963618..80963643,-	p15@TPD52
Hg19::chr8:80963645..80963656,-	p22@TPD52
Hg19::chr8:80963666..80963669,-	p37@TPD52
Hg19::chr8:80963673..80963679,-	p29@TPD52
Hg19::chrX:2420841..2420865,-	p4@DHRSX
Hg19::chrX:2420871..2420883,-	p6@DHRSX
Hg19::chrX:57619447..57619495,+	p2@ZXDB

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:0043085	positive regulation of catalytic activity	0.00666478581887981
GO:0032147	activation of protein kinase activity	0.0144788471296079
GO:0046982	protein heterodimerization activity	0.0159147723705919
GO:0050790	regulation of catalytic activity	0.0159147723705919
GO:0065009	regulation of a molecular function	0.0159147723705919
GO:0045860	positive regulation of protein kinase activity	0.0159147723705919
GO:0033674	positive regulation of kinase activity	0.0159147723705919
GO:0051347	positive regulation of transferase activity	0.0159147723705919
GO:0042803	protein homodimerization activity	0.0163259198672619
GO:0004035	alkaline phosphatase activity	0.020550845677255
GO:0050700	CARD domain binding	0.023967518948923
GO:0045859	regulation of protein kinase activity	0.023967518948923
GO:0043549	regulation of kinase activity	0.023967518948923
GO:0051338	regulation of transferase activity	0.023967518948923
GO:0046339	diacylglycerol metabolic process	0.023967518948923
GO:0008635	caspase activation via cytochrome c	0.0288826181170591
GO:0007250	activation of NF-kappaB-inducing kinase	0.0362320546560548
GO:0042802	identical protein binding	0.0404723163106256
GO:0046983	protein dimerization activity	0.0404723163106256

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
larynx	9.93e-127	9
upper respiratory tract	5.23e-60	19
respiratory primordium	6.65e-30	38
endoderm of foregut	6.65e-30	38
segment of respiratory tract	4.03e-24	47
respiratory tract	5.96e-21	54
respiratory system	3.49e-15	74
foregut	7.56e-13	87
organ segment	2.37e-11	98
subdivision of digestive tract	2.95e-09	118
digestive system	1.93e-07	145
digestive tract	1.93e-07	145
primitive gut	1.93e-07	145
primordium	9.78e-07	160

Disease

Ontology term	p-value	n
carcinoma	2.37e-16	106
cell type cancer	5.90e-12	143
cancer	1.45e-08	235
disease of cellular proliferation	2.27e-08	239

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	14	2.47991259470105	0.000875307488389353	0.00652926496535217
GATA3#2625	8	4.84204735239218	0.000210080933559813	0.00244518473420855
NR3C1#2908	8	2.66187081443076	0.00919296143112836	0.0347674705379546
STAT3#6774	12	2.8051906659078	0.000780188278743122	0.00611268444438506

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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