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{{Coexpression_clusters
{
|full_id=C2089_pharyngeal_epidermoid_Hep2_rectal_Prostate_gastric_Adipocyte

Latest revision as of 11:58, 17 September 2013


Full id: C2089_pharyngeal_epidermoid_Hep2_rectal_Prostate_gastric_Adipocyte



Phase1 CAGE Peaks

Hg19::chr11:101980713..101980754,+p8@YAP1
Hg19::chr11:101981327..101981348,+p7@YAP1
Hg19::chr11:101981353..101981380,+p5@YAP1
Hg19::chr11:101981423..101981503,+p3@YAP1


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
fibroblast1.56e-0976
epithelial cell2.55e-08253
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.61e-17160
endoderm1.61e-17160
presumptive endoderm1.61e-17160
digestive system1.87e-15145
digestive tract1.87e-15145
primitive gut1.87e-15145
organism subdivision8.64e-15264
multi-tissue structure2.08e-14342
multi-cellular organism8.08e-12656
organ component layer5.61e-1166
trunk1.40e-10199
subdivision of digestive tract7.66e-10118
reproductive structure1.36e-0959
reproductive system1.36e-0959
mesenchyme1.65e-09160
entire embryonic mesenchyme1.65e-09160
primordium2.06e-09160
surface structure8.51e-0999
reproductive organ1.09e-0748
larynx1.12e-079
organ1.19e-07503
orifice1.29e-0736
anatomical system1.66e-07624
trunk mesenchyme1.95e-07122
anatomical group2.69e-07625
respiratory system3.92e-0774
immaterial anatomical entity4.00e-07117
anatomical cluster6.32e-07373
Disease
Ontology termp-valuen
cell type cancer2.66e-09143
carcinoma1.72e-08106


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.15.26462
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
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
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
MA0135.11.23748
MA0136.11.94315
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.12.31379
MA0147.10.46175
MA0148.10.739888
MA0149.110.511
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.65877
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.24.43857
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
BHLHE40#8553222.43590677348870.002891464496853120.0156361860190982
E2F4#187439.501045236463330.001850751034728270.010923457887312
EP300#203335.08045629466740.01144298405398240.0418655437404143
GABPB1#255335.300762877136630.01012678824234270.0378360690173517
GATA3#2625320.42738726790450.0001924415576258320.00231868987504433
HEY1#2346244.040111043105710.00375304636917980.0185475043652472
MAX#414934.839416631755340.01315737137836840.0465874257318082
STAT3#677437.889598747865680.003190760481680130.0167373095904667
TAF1#687243.343046285745290.008005664898701650.0321158345377392
TCF7L2#693438.077632422353010.002978381685834620.0158558061416496
TFAP2A#7020416.5186343730451.34240829060362e-050.00032581868338915
TFAP2C#7022410.80922860986027.32289634782688e-050.00114336368914739
TRIM28#10155418.59052504526258.36730015875654e-060.000229664247379862



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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