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Coexpression cluster:C4792

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Full id: C4792_small_left_aorta_carcinoid_MCF7_adenocarcinoma_Renal



Phase1 CAGE Peaks

  Short description
Hg19::chr9:116225978..116225998,+ p12@RGS3
Hg19::chr9:116225999..116226029,+ p4@RGS3
Hg19::chr9:116226039..116226056,+ p11@RGS3


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 cell1.52e-24253
kidney cell7.94e-0917
kidney epithelial cell7.94e-0917
kidney tubule cell1.27e-0810
nephron tubule epithelial cell1.27e-0810
epithelial cell of nephron1.18e-0715
Uber Anatomy
Ontology termp-valuen
anatomical cluster1.23e-16373
digestive system2.29e-16145
digestive tract2.29e-16145
primitive gut2.29e-16145
subdivision of digestive tract4.08e-16118
organ system subdivision6.52e-16223
endoderm-derived structure3.03e-14160
endoderm3.03e-14160
presumptive endoderm3.03e-14160
trunk region element4.29e-14101
multi-tissue structure1.81e-13342
organ part1.43e-11218
endo-epithelium7.45e-1182
organ segment2.00e-1098
foregut5.80e-1087
subdivision of trunk1.01e-09112
primordium2.28e-09160
respiratory primordium2.86e-0938
endoderm of foregut2.86e-0938
nephron tubule epithelium1.27e-0810
cavitated compound organ4.38e-0831
excretory tube4.75e-0816
kidney epithelium4.75e-0816
immaterial anatomical entity7.90e-08117
lung8.57e-0822
respiratory tube8.57e-0822
respiration organ8.57e-0822
pair of lungs8.57e-0822
lung primordium8.57e-0822
lung bud8.57e-0822
epithelial bud1.03e-0737
nephron epithelium1.18e-0715
renal tubule1.18e-0715
nephron tubule1.18e-0715
nephron1.18e-0715
uriniferous tubule1.18e-0715
nephrogenic mesenchyme1.18e-0715
tube1.42e-07192
epithelium1.53e-07306
kidney2.00e-0726
kidney mesenchyme2.00e-0726
upper urinary tract2.00e-0726
kidney rudiment2.00e-0726
kidney field2.00e-0726
cell layer2.13e-07309
abdomen element2.29e-0754
abdominal segment element2.29e-0754
organ2.45e-07503
segment of respiratory tract2.48e-0747
epithelial fold2.88e-0747
respiratory tract5.66e-0754
gastrointestinal system6.01e-0725
thoracic cavity element6.89e-0734
thoracic cavity6.89e-0734
urinary system structure7.52e-0747
Disease
Ontology termp-valuen
carcinoma6.28e-35106
cell type cancer5.75e-30143
cancer2.11e-15235
disease of cellular proliferation2.53e-14239
adenocarcinoma4.47e-1325
respiratory system cancer7.46e-0916
lung cancer2.08e-0815
gastrointestinal system cancer3.34e-0714
bronchus cancer8.73e-077
bronchogenic carcinoma8.73e-077


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
MA0061.11.15625
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
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.15.93331
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.14.51393
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.22.38017
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
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
MA0099.20.902716
MA0079.20.69213
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
CTCF#1066435.360256373075030.0064925092527670.0281637802728748
E2F1#186934.907389214879320.008460985347239390.0328118840251136
E2F4#1874312.66806031528440.0004917987006298980.00439337648576563
E2F6#187635.017155731697390.00791769806886330.032471391997723
EP300#203336.77394172622320.003216880500103790.0168607739912848
ZNF263#1012738.221841637010680.001799043925565870.0110212546071196



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.