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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0.

Latest revision as of 12:04, 17 September 2013


Full id: C2376_esophagus_amniotic_throat_tonsil_tongue_salivary_endometrioid



Phase1 CAGE Peaks

Hg19::chr16:4940321..4940338,-p@chr16:4940321..4940338
-
Hg19::chr16:4987129..4987156,-p1@PPL
Hg19::chr16:4987174..4987185,-p3@PPL
Hg19::chr16:4987202..4987221,-p2@PPL


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 cell2.08e-23253
endo-epithelial cell2.14e-1642
endodermal cell7.73e-1458
epithelial cell of alimentary canal2.96e-0920
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.59e-19160
endoderm2.59e-19160
presumptive endoderm2.59e-19160
digestive system2.51e-17145
digestive tract2.51e-17145
primitive gut2.51e-17145
respiratory system1.17e-1674
organ part2.21e-15218
organ4.27e-15503
subdivision of digestive tract4.39e-14118
multi-tissue structure3.05e-13342
respiratory tract1.61e-1154
multi-cellular organism4.85e-11656
anatomical space5.91e-1195
foregut9.64e-1187
organ system subdivision2.40e-10223
immaterial anatomical entity3.24e-10117
thoracic segment organ3.51e-1035
thoracic cavity element6.66e-1034
thoracic cavity6.66e-1034
adult organism1.14e-09114
segment of respiratory tract4.18e-0947
trunk region element7.99e-09101
anatomical system1.33e-08624
primordium1.41e-08160
respiratory primordium1.62e-0838
endoderm of foregut1.62e-0838
anatomical group1.85e-08625
epithelial fold2.28e-0847
orifice2.66e-0836
oral opening3.89e-0822
anatomical cluster5.14e-08373
endo-epithelium6.12e-0882
organ segment8.09e-0898
embryo1.27e-07592
epithelial bud1.34e-0737
organism subdivision1.45e-07264
thoracic segment of trunk5.95e-0752
tracheobronchial tree9.24e-0715
lower respiratory tract9.24e-0715
Disease
Ontology termp-valuen
carcinoma3.59e-18106
cell type cancer9.62e-11143
adenocarcinoma9.65e-0825
squamous cell carcinoma9.29e-0714


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
MA0007.10.6918
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
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.11.47051
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
MA0073.10.380957
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
MA0101.10.539569
MA0103.11.29536
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
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
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.13.58384
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.23.66694
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.13.50007
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.97967
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
ESR1#2099323.07645247211590.0001339105244968570.0017576324328173
HNF4A#3172317.34921777221530.0003125641557482750.00321487963976699
HNF4G#3174321.56506689483510.0001638032421292610.00203611602055913
ZBTB7A#5134135.513931980906920.009038352821081090.0342348141399517



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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