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Coexpression cluster:C3317: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129139881664053!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167073341563648!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000674638957390369!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00390268910603454!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443415149822244!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015635321740954!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000735319662829854!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308248866951455!POU5F1#5460;3:335.439201451906:2.63510205045339e-08:1.82015491433401e-06!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00164930916114905!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275816470940551!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245758528458139!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541346491061006!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00628215130607564!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189748953781312
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129139881664053!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167073341563648!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000674638957390369!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00390268910603454!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443415149822244!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015635321740954!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000735319662829854!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308248866951455!POU5F1#5460;3:335.439201451906:2.63510205045339e-08:1.82015491433401e-06!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00164930916114905!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275816470940551!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245758528458139!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541346491061006!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00628215130607564!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189748953781312
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}}
}}

Revision as of 16:03, 26 November 2012


Full id: C3317_smallcell_lung_merkel_small_kidney_bronchioalveolar_Renal



Phase1 CAGE Peaks

Hg19::chr12:6484605..6484629,-p1@SCNN1A
Hg19::chr12:6484687..6484698,-p6@SCNN1A
Hg19::chr12:6484722..6484736,-p2@SCNN1A


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


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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.19e-24160
endoderm4.19e-24160
presumptive endoderm4.19e-24160
subdivision of digestive tract1.64e-19118
digestive system5.21e-19145
digestive tract5.21e-19145
primitive gut5.21e-19145
trunk region element1.06e-15101
anatomical space2.54e-1595
immaterial anatomical entity4.19e-15117
renal system1.48e-1448
urinary system structure6.58e-1447
endo-epithelium5.84e-1382
respiratory system2.06e-1274
epithelial bud4.08e-1237
thoracic cavity element1.34e-1134
thoracic cavity1.34e-1134
foregut1.50e-1187
respiratory tract3.88e-1154
organ4.68e-11503
thoracic segment organ4.86e-1135
lung1.22e-0922
respiratory tube1.22e-0922
respiration organ1.22e-0922
pair of lungs1.22e-0922
lung primordium1.22e-0922
lung bud1.22e-0922
epithelial fold2.24e-0947
reproductive structure6.44e-0959
reproductive system6.44e-0959
nephron tubule epithelium6.52e-0910
subdivision of trunk1.58e-08112
organ system subdivision2.18e-08223
respiratory primordium3.63e-0838
endoderm of foregut3.63e-0838
embryo4.47e-08592
multi-cellular organism5.44e-08656
organism subdivision5.86e-08264
male organism6.33e-0822
male reproductive system6.33e-0822
organ part8.31e-08218
reproductive organ1.30e-0748
male reproductive organ1.33e-0711
kidney1.34e-0726
kidney mesenchyme1.34e-0726
upper urinary tract1.34e-0726
kidney rudiment1.34e-0726
kidney field1.34e-0726
orifice2.08e-0736
cavitated compound organ2.15e-0731
respiratory tract epithelium2.75e-0719
lung epithelium2.75e-0719
segment of respiratory tract3.52e-0747
multi-tissue structure3.54e-07342
excretory tube3.71e-0716
kidney epithelium3.71e-0716
respiratory system epithelium3.74e-0728
organ segment8.18e-0798
Disease
Ontology termp-valuen
carcinoma1.14e-16106
cell type cancer1.67e-11143
adenocarcinoma1.55e-0725


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)

{{{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


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

TF#promotersEnrichmentp-valueq-value
CTBP2#1488362.71700033932814.049570681927e-060.000129139881664053
EP300#203336.77394172622320.003216880500103790.0167073341563648
ESR1#2099330.76860329615453.43136389821584e-050.000674638957390369
HDAC2#3066313.41562023662630.0004140761399857210.00390268910603454
JUN#3725312.51282919233630.0005103313992726250.00443415149822244
JUND#372736.994663941871030.002921845042734990.015635321740954
NANOG#79923329.24477848101273.99627955670032e-050.000735319662829854
NR3C1#2908314.9730233311730.0002978331194675480.00308248866951455
POU5F1#54603335.4392014519062.63510205045339e-081.82015491433401e-06
RXRA#6256320.07461713913330.0001235730348432220.00164930916114905
SIN3A#2594235.408884726815140.006318961977991520.0275816470940551
SP1#666735.69838137814090.005403962701712170.0245758528458139
TAF7#6879311.43306940492390.0006690181981945830.00541346491061006
TCF12#6938310.63446490218640.0008313523990202070.00628215130607564
USF1#739136.361499277207960.00388404057290560.0189748953781312



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.