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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.224223362570709,

Latest revision as of 12:18, 17 September 2013


Full id: C3068_epidermoid_pharyngeal_aorta_amniotic_chorionic_Hep2_mature



Phase1 CAGE Peaks

Hg19::chr11:101980791..101980865,+p4@YAP1
Hg19::chr11:101981127..101981164,+p2@YAP1
Hg19::chr11:101981169..101981187,+p1@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><br>

Cell Type
Ontology termp-valuen
fibroblast9.20e-1376
endodermal cell1.62e-0858
epithelial cell1.60e-07253
skin fibroblast1.82e-0723
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.53e-22160
endoderm2.53e-22160
presumptive endoderm2.53e-22160
digestive system1.39e-19145
digestive tract1.39e-19145
primitive gut1.39e-19145
multi-tissue structure1.05e-16342
surface structure1.19e-1699
organism subdivision1.97e-15264
multi-cellular organism6.92e-14656
subdivision of digestive tract1.43e-12118
primordium7.67e-11160
trunk1.03e-10199
mesenchyme1.59e-10160
entire embryonic mesenchyme1.59e-10160
organ2.62e-10503
anatomical system3.69e-10624
anatomical group5.59e-10625
immaterial anatomical entity2.69e-09117
organ component layer2.95e-0966
trunk mesenchyme3.83e-09122
orifice1.23e-0836
anatomical cluster2.41e-08373
respiratory system2.58e-0874
reproductive structure3.91e-0859
reproductive system3.91e-0859
larynx1.50e-079
endo-epithelium2.03e-0782
organ part2.68e-07218
mouth2.93e-0729
stomodeum2.93e-0729
integument4.65e-0746
integumental system4.65e-0746
gut epithelium5.01e-0754
foregut5.16e-0787
skin of body6.76e-0741
anatomical space8.15e-0795


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)
MA0003.11.0927
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.16.40038
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#8553344.87181354697741.10603738662898e-050.000283677403296032
CEBPB#105137.971147625824820.001974187055288560.0114909503353554
E2F1#186934.907389214879320.008460985347239390.0323553457830301
E2F4#1874312.66806031528440.0004917987006298980.0043539005251408
E2F6#187635.017155731697390.00791769806886330.0320361253918338
EP300#203336.77394172622320.003216880500103790.0166841030218175
FOXA1#3169311.08141974938550.000734755275698670.00579366600518636
GATA3#2625218.15767757147070.003944546819279620.0189408977130457
MAX#414936.452555509007120.003721913834265510.0185711604288785
MXI1#460139.96157162875930.001011470541259020.00718081516270485
SMC3#9126210.02995522995520.0126656379767470.0457047392942257
TCF7L2#6934310.77017656313730.0008003181298398380.00611667948498667
TFAP2A#7020316.5186343730450.0002218033880766340.00247329959933115
TFAP2C#7022310.80922860986020.0007916746575753130.00612911116104582
TRIM28#10155318.59052504526250.0001555969297255280.0019654557019357
USF1#739136.361499277207960.00388404057290560.0189483049978367
USF2#7392312.99219738506960.0004558979393427810.00420354241079021



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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