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Coexpression cluster:C1089: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1089_Smooth_Small_Fibroblast_Prostate_anaplastic_mesenchymal_nasal
|id=C1089
}}

Latest revision as of 11:37, 17 September 2013


Full id: C1089_Smooth_Small_Fibroblast_Prostate_anaplastic_mesenchymal_nasal



Phase1 CAGE Peaks

Hg19::chr6:83073334..83073351,+p8@TPBG
Hg19::chr6:83073396..83073408,+p5@TPBG
Hg19::chr6:83073511..83073522,+p6@TPBG
Hg19::chr6:83073525..83073551,+p1@TPBG
Hg19::chr6:83073553..83073601,+p2@TPBG
Hg19::chr6:83073952..83074004,+p3@TPBG
Hg19::chr6:83074008..83074024,+p9@TPBG
Hg19::chr6:83074273..83074294,+p@chr6:83074273..83074294
+


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
organism subdivision1.91e-18264
surface structure9.84e-1799
multilaminar epithelium1.80e-1683
trunk4.64e-15199
multi-cellular organism1.27e-13656
somite1.91e-1371
presomitic mesoderm1.91e-1371
presumptive segmental plate1.91e-1371
dermomyotome1.91e-1371
trunk paraxial mesoderm1.91e-1371
dense mesenchyme tissue2.77e-1373
paraxial mesoderm5.65e-1372
presumptive paraxial mesoderm5.65e-1372
epithelial vesicle4.27e-1278
skeletal muscle tissue9.19e-1162
striated muscle tissue9.19e-1162
myotome9.19e-1162
trunk mesenchyme9.44e-11122
muscle tissue1.08e-1064
musculature1.08e-1064
musculature of body1.08e-1064
multi-tissue structure1.85e-10342
organ component layer2.35e-1066
mesenchyme3.51e-10160
entire embryonic mesenchyme3.51e-10160
anatomical system1.15e-09624
anatomical group1.47e-09625
reproductive structure1.18e-0859
reproductive system1.18e-0859
systemic artery1.51e-0833
systemic arterial system1.51e-0833
integument1.78e-0846
integumental system1.78e-0846
artery1.81e-0842
arterial blood vessel1.81e-0842
arterial system1.81e-0842
unilaminar epithelium2.26e-08148
cell layer3.76e-08309
epithelium5.58e-08306
female organism8.66e-0841
skin of body1.09e-0741
endoderm-derived structure1.25e-07160
endoderm1.25e-07160
presumptive endoderm1.25e-07160
embryo4.26e-07592
orifice5.73e-0736
splanchnic layer of lateral plate mesoderm7.53e-0783
anatomical space9.58e-0795
Disease
Ontology termp-valuen
ovarian cancer3.04e-0814


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)
MA0003.10.248189
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.727045
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.12.32702
MA0029.10.832916
MA0030.11.92084
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.11.2107
MA0056.10
MA0057.15.82891
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.12.19078
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.12.60013
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.131075
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.13.68539
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.11.49614
MA0103.10.291333
MA0105.11.47197
MA0106.10.59853
MA0107.12.69808
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.11.49247
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.11.60834
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.17.19659
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.113833
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.942487
MA0035.20.515566
MA0039.20.881644
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.22.44381
MA0112.20.0572179
MA0065.20.844872
MA0150.11.00335
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.43752
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.93331
MA0163.10.0104024
MA0164.10.627336
MA0080.20.818924
MA0018.20.599912
MA0099.20.523145
MA0079.210.5497
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
MA0442.10



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
CTCF#1066464.020192279806270.0008334820206774180.00629005193710014
E2F1#186963.680541911159490.001366491550819140.008992754321109
EP300#203354.23371357888950.002652037544592280.0146385576406994
FOXA1#316956.925887343365910.0002650891078941710.0028380975232557
POLR2A#543082.147453176558070.002210725788971910.0127258992820612
POU2F2#545255.691327536089080.000670954773528490.00541570798303903
RAD21#588556.47189618466020.0003657753484789720.00365002977448838
SMARCC2#6601558.8471090168117.33198250050869e-095.68904101315473e-07
SMC3#912659.403083028083036.12099279950925e-050.00100403701427351
TAF1#687272.925165500027130.001265325357915740.00849288657168136
TAF7#687957.145668378077450.0002284466637700410.00251993463429228
ZNF263#1012755.138651023131670.001082531249033560.00763960275138965



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.

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