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Coexpression cluster:C341: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;12:2.46325153680844:0.00181435430642365:0.0108983349288882!RAD21#5885;12:3.76546687107503:3.32121315067201e-05:0.000660065043278848!STAT3#6774;8:2.55017333264345:0.0105509167498914:0.0389897103687606!TCF7L2#6934;12:3.91642784114085:2.23995125295158e-05:0.000490025699428174
|tf_chipseq_enrich=EP300#2033;12:2.46325153680844:0.00181435430642365:0.0108983349288882!RAD21#5885;12:3.76546687107503:3.32121315067201e-05:0.000660065043278848!STAT3#6774;8:2.55017333264345:0.0105509167498914:0.0389897103687606!TCF7L2#6934;12:3.91642784114085:2.23995125295158e-05:0.000490025699428174
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|tfbs_overrepresentation_for_novel_motifs=0.0391464,0.00254248,0.146286,1.06548,0.495643,0.634731,0.13057,0.0995429,0.208201,0.000202207,0.0780977,0.155358,0.017752,0.392606,2.55059,0.303553,0.274123,0.0147216,0.00365927,0.648082,0.339391,0.0444592,0.0881331,0.105169,0.192249,0.169033,0.518265,0.293913,0.111883,1.15562,0.520703,0.301321,0.479525,0.136379,0.0183975,3.0954e-05,0.0177865,0.0922784,0.171279,0.0259523,0.401415,0.062417,0.412896,0.783873,0.322092,0.0465565,0.131171,0.2558,1.08348,0.270954,0.177819,0.137739,0.0423185,0.360536,0.486376,0.125892,0.516012,0.108703,0.0815711,0.108193,0.332512,0.132479,0.851117,0.254197,0.142578,0.651245,0.562972,0.901485,0.293563,0.749341,0.0574197,0.894411,0.00357758,0.48467,0.00266031,0.35094,0.681879,0.679569,4.98706,1.12226,1.30036,0.705404,0.862965,0.607891,1.12338,1.78248e-06,0.00194292,0.0299496,0.19436,0.996295,0.646289,0.418934,0.314004,0.503644,0.0260292,0.829334,0.455633,0.346841,0.197346,0.123091,0.0657404,0.833695,0.342487,0.276796,0.222295,0.0761449,0.265312,3.19942,0.191981,0.0222238,0.0403126,0.340332,0.329154,0.0822381,0.603172,0.392926,0.00482095,0.518154,0.647486,0.0112259,0.477624,0.562637,0.628534,0.455006,0.703324,0.242821,0.399788,0.317804,0.514129,1.16897,0.419503,0.0700713,0.526577,1.41918,0.657947,0.0264802,0.87165,0.0873984,0.619678,1.43971,1.0467,0.586378,0.128038,0.344087,0.223488,0.104448,0.212265,1.2832,0.0611342,0.287878,0.0734517,4.98319e-05,2.82524,0.0297034,0.132211,1.83091,0.184011,0.242525,0.0517159,0.042112,0.585299,0.404642,0.290564,0.0431301,0.234512,2.00234,0.126256,0.406823,3.09231e-05
}}
}}

Revision as of 14:08, 26 November 2012


Full id: C341_giant_large_Fibroblast_Mesenchymal_Alveolar_Mesothelial_mesothelioma



Phase1 CAGE Peaks

Hg19::chr10:4828673..4828695,+p10@AKR1E2
Hg19::chr10:4828763..4828786,+p7@AKR1E2
Hg19::chr10:4828815..4828822,+p11@AKR1E2
Hg19::chr10:4828859..4828883,+p6@AKR1E2
Hg19::chr10:4832416..4832424,-p@chr10:4832416..4832424
-
Hg19::chr11:28723970..28723983,+p3@ENST00000513853
Hg19::chr11:28724030..28724037,+p6@ENST00000513853
Hg19::chr12:120662266..120662274,-p65@PXN
Hg19::chr12:120662499..120662559,-p3@PXN
Hg19::chr12:120662701..120662711,-p58@PXN
Hg19::chr12:120662730..120662751,-p46@PXN
Hg19::chr12:26126668..26126674,+p27@RASSF8
Hg19::chr12:26126681..26126692,+p8@RASSF8
Hg19::chr12:66035928..66035945,-p1@ENST00000535315
p1@ENST00000537298
Hg19::chr12:66035968..66035976,-p1@ENST00000537250
Hg19::chr12:66035982..66035985,-p3@ENST00000537250
Hg19::chr12:66035988..66035995,-p2@ENST00000537250
Hg19::chr12:66036060..66036071,-p4@ENST00000539653
Hg19::chr12:66036083..66036098,-p3@ENST00000539653
Hg19::chr12:66036125..66036136,-p2@ENST00000539653
Hg19::chr12:66036137..66036157,-p1@ENST00000539653
p2@ENST00000544557
Hg19::chr12:66036191..66036200,-p3@ENST00000544557
Hg19::chr12:66036219..66036262,-p1@ENST00000544557
Hg19::chr15:33384526..33384543,-p@chr15:33384526..33384543
-
Hg19::chr15:33384561..33384569,-p@chr15:33384561..33384569
-
Hg19::chr1:172902742..172902768,-p@chr1:172902742..172902768
-
Hg19::chr2:239344630..239344631,+p20@ASB1
Hg19::chr2:36805997..36806020,-p10@FEZ2
Hg19::chr2:36806173..36806191,-p14@FEZ2
Hg19::chr2:36806197..36806224,-p11@FEZ2
Hg19::chr2:36806228..36806237,-p24@FEZ2
Hg19::chr2:36806248..36806258,-p23@FEZ2
Hg19::chr5:14200357..14200390,+p@chr5:14200357..14200390
+


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


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


GO IDGO nameFDR corrected p-value
GO:0007165signal transduction0.0175341130992519
GO:0017166vinculin binding0.0175341130992519
GO:0007154cell communication0.0175341130992519
GO:0051674localization of cell0.0175341130992519
GO:0006928cell motility0.0175341130992519
GO:0030539male genitalia development0.0206567778714676
GO:0048806genitalia development0.0236046189169336
GO:0042036negative regulation of cytokine biosynthetic process0.0244745405962095
GO:0007172signal complex assembly0.0244745405962095
GO:0046546development of primary male sexual characteristics0.0357782122939305
GO:0046661male sex differentiation0.0400209603080005
GO:0017148negative regulation of translation0.0469851050101578
GO:0031327negative regulation of cellular biosynthetic process0.047384859189351
GO:0009890negative regulation of biosynthetic process0.047384859189351
GO:0007411axon guidance0.047384859189351
GO:0045137development of primary sexual characteristics0.047384859189351
GO:0042035regulation of cytokine biosynthetic process0.047384859189351
GO:0042089cytokine biosynthetic process0.047384859189351
GO:0042107cytokine metabolic process0.047384859189351
GO:0043623cellular protein complex assembly0.047384859189351



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><br>disease_data<br>


Disease
Ontology termp-valuen
lung large cell carcinoma5.96e-343
non-small cell lung carcinoma5.15e-215
lung carcinoma2.45e-129
lung cancer5.93e-0815
respiratory system cancer1.54e-0716


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


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

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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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EP300#2033122.463251536808440.001814354306423650.0108983349288882
RAD21#5885123.765466871075033.32121315067201e-050.000660065043278848
STAT3#677482.550173332643450.01055091674989140.0389897103687606
TCF7L2#6934123.916427841140852.23995125295158e-050.000490025699428174



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


This analysis result is provided for C0 - C305 clusters.