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Coexpression cluster:C2832: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2832_iPS_mesothelioma_testicular_teratocarcinoma_H9_HES3GFP_giant
|id=C2832
}}

Latest revision as of 12:13, 17 September 2013


Full id: C2832_iPS_mesothelioma_testicular_teratocarcinoma_H9_HES3GFP_giant



Phase1 CAGE Peaks

Hg19::chr5:89770664..89770688,+p2@POLR3G
Hg19::chr5:89770696..89770727,+p1@POLR3G
Hg19::chr5:89770738..89770749,+p4@POLR3G
Hg19::chr5:89797743..89797759,+p@chr5:89797743..89797759
+


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>

Cell Type
Ontology termp-valuen
epithelial cell1.05e-18253
embryonic cell1.23e-10250
Uber Anatomy
Ontology termp-valuen
cell layer4.57e-08309
epithelium7.21e-08306
Disease
Ontology termp-valuen
disease of cellular proliferation1.80e-25239
cancer8.70e-25235
hematologic cancer1.30e-1251
immune system cancer1.30e-1251
cell type cancer1.96e-11143
organ system cancer3.09e-11137
leukemia5.28e-1039
carcinoma9.34e-09106
myeloid leukemia5.25e-0731


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)
MA0003.10.720743
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.12.76745
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.12.4958
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.23.52208
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
CCNT2#90534.752151182721970.01386206996689490.0487389148017955
CHD2#110637.758017125587640.003351522464536340.0173076371970783
ETS1#211337.296570691651750.00400857377511390.0192112443327423
GTF2F1#296239.554745657568240.001820362319304780.010903069350569
HDAC2#3066310.06171517746970.00156372754474740.00992670441562568
HMGN3#932436.133910792512940.006640696683324720.0283103812927484
IRF1#365935.727872815172930.008097114790333330.032019028873864
MAX#414934.839416631755340.01315737137836840.0466443553762869
MEF2A#4205314.0574231822330.0005830038854186610.00488984442573398
MXI1#460137.471178721569470.003741314738550960.0186421359723055
NANOG#79923321.93358386075950.0001557535816382770.00196577018884834
NRF1#489939.157709585783180.002061953791733420.011966458771663
PAX5#507935.002174148383370.01196533174786410.0435204876511519
POU2F2#545236.829593043306890.004860473775203740.0227756200919106
REST#597837.237521537096020.004104697304192610.0195910100426182
TAF7#687938.574802053692940.00250055433515240.0140391030109118
TCF12#693837.975848676639820.003090920396013070.0162888603915233
TFAP2C#702238.106921457395170.002947011739866440.0157192522522937
THAP1#55145215.68457230142570.005840469678357920.0262511969675513
TRIM28#10155313.94289378394690.0005972858184258420.004997190866825
USF1#739134.771124457905970.01370465887188020.0483335314868569
ZBTB33#10009323.74854377248590.0001229451908818380.00165638193892006
ZNF143#7702310.12565741417090.001534861610688180.00977077970002824
ZNF263#1012736.166381227758010.006539814347975980.0279899873243285



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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