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Coexpression cluster:C4317

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Full id: C4317_renal_squamous_bile_glassy_epidermoid_epithelioid_malignant



Phase1 CAGE Peaks

  Short description
Hg19::chr3:194040528..194040540,- p@chr3:194040528..194040540
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Hg19::chr3:194040578..194040593,- p@chr3:194040578..194040593
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Hg19::chr3:194040598..194040638,- p@chr3:194040598..194040638
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Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
epithelial cell5.07e-39253
endo-epithelial cell9.93e-1542
endodermal cell3.07e-1458
epithelial cell of alimentary canal2.26e-1120
squamous epithelial cell8.08e-0963
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.18e-18160
endoderm6.18e-18160
presumptive endoderm6.18e-18160
digestive system1.11e-16145
digestive tract1.11e-16145
primitive gut1.11e-16145
larynx1.98e-149
subdivision of digestive tract3.71e-14118
foregut1.62e-1387
upper respiratory tract7.23e-1219
respiratory system1.16e-1074
segment of respiratory tract1.43e-1047
respiratory tract2.70e-1054
respiratory primordium2.96e-0938
endoderm of foregut2.96e-0938
biliary system1.42e-089
biliary tree1.42e-089
biliary bud1.42e-089
orifice2.36e-0736
viscus8.18e-0718
Disease
Ontology termp-valuen
carcinoma3.28e-50106
cell type cancer5.02e-37143
cancer3.06e-25235
disease of cellular proliferation3.26e-24239
adenocarcinoma1.75e-1725
squamous cell carcinoma6.35e-1614


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.12.72668
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
MA0055.11.06172
MA0056.10
MA0057.10.886807
MA0058.10.716037
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
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
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
MA0144.12.26598
MA0145.11.37817
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
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
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.22.08754
MA0079.20.09178
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105137.971147625824820.001974187055288560.0115547030860391
E2F1#186934.907389214879320.008460985347239390.03266632836791
EP300#203336.77394172622320.003216880500103790.0167967094565713
ESR1#2099330.76860329615453.43136389821584e-050.000678470681873843
FOS#235338.99795530889440.001372499272417130.00899996556237663
FOSL1#8061339.7135797163731.59554825631833e-050.000371875617812163
FOSL2#2355316.93020060456170.0002060162053171620.00243615562354156
GATA1#2623313.56030814380040.0004009615963782630.00388784961137772
GTF2F1#2962312.73966087675770.0004835525047438590.00435059786724189
JUN#3725312.51282919233630.0005103313992726250.00445378967231835
JUND#372736.994663941871030.002921845042734990.0157223233766912
MAX#414936.452555509007120.003721913834265510.018709711154065
MXI1#460139.96157162875930.001011470541259020.00721859859632028
MYC#460935.22228187160940.007020843755740150.0295427035054692
NR3C1#2908314.9730233311730.0002978331194675480.00309598817199873
SMARCC1#6599343.66335931963151.20046018043203e-050.000302108098275038
SMC3#9126315.04493284493280.0002935825420371870.00310024945478481
STAT3#6774310.51946499715420.0008589184530415310.0064438319314133
TFAP2A#7020316.5186343730450.0002218033880766340.0024895135999286
TFAP2C#7022310.80922860986020.0007916746575753130.00617534614702428
TRIM28#10155318.59052504526250.0001555969297255280.00197597127232543



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.