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{{Coexpression_clusters
{
|full_id=C2876_squamous_gastric_pharyngeal_renal_signet_papillotubular_gall
 

Latest revision as of 12:14, 17 September 2013


Full id: C2876_squamous_gastric_pharyngeal_renal_signet_papillotubular_gall



Phase1 CAGE Peaks

Hg19::chr7:116312352..116312368,+p6@MET
Hg19::chr7:116312411..116312502,+p1@MET
Hg19::chr7:116312521..116312532,+p4@MET
Hg19::chr7:116312540..116312549,+p14@MET


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 cell5.46e-43253
embryonic cell2.74e-16250
endo-epithelial cell1.68e-1342
endodermal cell6.83e-1358
squamous epithelial cell3.42e-1163
columnar/cuboidal epithelial cell1.16e-0727
Uber Anatomy
Ontology termp-valuen
anatomical system2.24e-12624
anatomical group4.00e-12625
endoderm-derived structure8.84e-11160
endoderm8.84e-11160
presumptive endoderm8.84e-11160
multi-cellular organism1.66e-09656
epithelium8.47e-09306
respiratory primordium1.71e-0838
endoderm of foregut1.71e-0838
organ2.27e-08503
cell layer3.01e-08309
multi-tissue structure6.38e-08342
endo-epithelium6.98e-0882
digestive system8.91e-08145
digestive tract8.91e-08145
primitive gut8.91e-08145
respiratory tract2.41e-0754
anatomical cluster2.81e-07373
respiratory system6.32e-0774
extraembryonic membrane7.73e-0714
membranous layer7.73e-0714
Disease
Ontology termp-valuen
carcinoma5.56e-15106
cell type cancer2.29e-12143


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)
MA0003.110.8437
MA0004.12.8475
MA0006.13.33615
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
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
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.10.248209
MA0058.12.50688
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
MA0073.10.0343867
MA0074.11.91637
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
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
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
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.221129
MA0147.15.25242
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.23.68813
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.13.7809
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.13.02177
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.22.35343
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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#8553444.87181354697742.46312701995675e-071.28816486147853e-05
CTCF#1066445.360256373075030.001211145381643620.00819825085964601
E2F1#186944.907389214879320.001724022357361790.0106800623394334
E2F6#187645.017155731697390.00157802193473060.00999315018441238
FOS#235348.99795530889440.0001525147711168630.00195417619686837
JUND#372746.994663941871030.000417684217818580.0039257129251939
MAX#414946.452555509007120.0005767613195645490.00486444120600839
MXI1#460149.96157162875930.0001015224754950450.00142742404661106
MYC#460945.22228187160940.001344309395272740.00889836030757316
NR3C1#2908414.9730233311731.98868032687801e-050.00044455433360191
TAF1#687243.343046285745290.008005664898701650.0323294268175509
TCF7L2#6934410.77017656313737.42969445082454e-050.00115744310672683
TFAP2A#7020416.5186343730451.34240829060362e-050.000327416579781297
TFAP2C#7022410.80922860986027.32289634782688e-050.00114885980422216
USF1#739146.361499277207960.0006105011399140830.00509022262106713
USF2#7392412.99219738506963.50833029870167e-050.000682957144578012



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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