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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0632418018961231,

Latest revision as of 12:10, 17 September 2013


Full id: C2683_pancreatic_colon_choriocarcinoma_hepatocellular_Hepatocyte_Prostate_liver



Phase1 CAGE Peaks

Hg19::chr2:208630791..208630796,-p@chr2:208630791..208630796
-
Hg19::chr2:208634399..208634439,-p2@FZD5
Hg19::chr2:208634441..208634461,-p4@FZD5
Hg19::chr2:208634471..208634492,-p3@FZD5


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 cell2.16e-20253
endodermal cell5.81e-1158
Uber Anatomy
Ontology termp-valuen
digestive system2.76e-13145
digestive tract2.76e-13145
primitive gut2.76e-13145
endoderm-derived structure3.03e-13160
endoderm3.03e-13160
presumptive endoderm3.03e-13160
trunk region element3.89e-13101
subdivision of digestive tract4.23e-13118
organ system subdivision1.19e-12223
endo-epithelium2.92e-1182
anatomical cluster1.70e-10373
foregut1.52e-0987
subdivision of trunk1.93e-09112
abdomen element9.26e-0954
abdominal segment element9.26e-0954
abdominal segment of trunk1.67e-0860
abdomen1.67e-0860
organ2.10e-08503
immaterial anatomical entity4.82e-08117
Disease
Ontology termp-valuen
carcinoma5.38e-22106
cell type cancer2.89e-17143
cancer4.51e-12235
disease of cellular proliferation3.04e-11239


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)
MA0003.12.92335
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.14.49713
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
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
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
MA0103.11.29536
MA0105.12.66951
MA0106.10.869173
MA0107.12.00595
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.01976
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.15.47627
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.12.41215
MA0146.11.75643
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.52211
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.13.50007
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.12283
MA0102.21.75932
MA0258.10.418966
MA0259.12.06681
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
BHLHE40#8553333.65386016023314.35025573591721e-050.000775185734180955
CCNT2#90546.336201576962630.0006203100587215640.00512941902001753
CTCFL#140690314.80985576923080.0004996291767563340.00441013958682004
EBF1#187936.679850134926750.005184294118278910.0240555577314258
ESR1#2099323.07645247211590.0001339105244968570.00175829535679246
ETS1#211337.296570691651750.00400857377511390.0192085999770186
FOSL2#2355312.69765045342130.000787568572975710.00616773201807214
FOXA1#316938.311064812039090.002740138182109850.0150382181608707
HDAC2#3066310.06171517746970.00156372754474740.00992610107857981
HNF4A#3172317.34921777221530.0003125641557482750.00321582975689036
HNF4G#3174321.56506689483510.0001638032421292610.00203708583052368
IRF1#365935.727872815172930.008097114790333330.0320141802607466
NFYB#4801312.56984494015230.000811456397697350.00619093394105585
NR3C1#2908311.22976749837980.001131672068063850.00775580412865154
PAX5#507935.002174148383370.01196533174786410.0435098806592798
POU5F1#5460183.85980036297640.01187154239091560.0432426065766195
RAD21#588537.766275421592250.0033411193858720.0172709942358487
RXRA#6256315.055962854350.0004758307997303580.00433944227148436
SMC3#9126311.28369963369960.001115802366868050.00765809840266365
TFAP2A#7020312.38897577978370.000846941303588430.00638194103935585
TFAP2C#702238.106921457395170.002947011739866440.0157184494714219
USF1#739134.771124457905970.01370465887188020.0483188463952566
ZBTB7A#5134135.513931980906920.009038352821081090.0342522054603174



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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