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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0.0842546465117019

Latest revision as of 12:16, 17 September 2013


Full id: C2967_lung_Hepatocyte_hepatoma_hepatocellular_liver_mesothelioma_Intestinal



Phase1 CAGE Peaks

Hg19::chr10:101542462..101542535,+p1@ABCC2
Hg19::chr10:101542550..101542573,+p5@ABCC2
Hg19::chr10:101542585..101542592,+p6@ABCC2


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
metabolising cell9.20e-1912
endopolyploid cell9.20e-1912
parenchymal cell9.20e-1912
polyploid cell9.20e-1912
hepatocyte9.20e-1912
epithelial cell1.07e-12253
melanocyte5.93e-0910
melanoblast5.93e-0910
endodermal cell6.01e-0958
Uber Anatomy
Ontology termp-valuen
larynx7.88e-249
subdivision of digestive tract1.94e-23118
epithelium of foregut-midgut junction3.67e-2025
anatomical boundary3.67e-2025
hepatobiliary system3.67e-2025
foregut-midgut junction3.67e-2025
septum transversum3.67e-2025
hepatic diverticulum4.72e-2022
liver primordium4.72e-2022
liver5.15e-2019
digestive gland5.15e-2019
liver bud5.15e-2019
digestive tract diverticulum4.92e-1923
digestive system1.54e-18145
digestive tract1.54e-18145
primitive gut1.54e-18145
foregut2.78e-1887
epithelial sac3.04e-1725
sac1.88e-1626
endoderm-derived structure7.03e-16160
endoderm7.03e-16160
presumptive endoderm7.03e-16160
abdomen element9.31e-1354
abdominal segment element9.31e-1354
abdominal segment of trunk2.38e-1260
abdomen2.38e-1260
gut epithelium1.01e-1154
exocrine gland3.94e-1131
exocrine system3.94e-1131
upper respiratory tract2.45e-1019
trunk region element4.65e-10101
respiratory primordium1.53e-0938
endoderm of foregut1.53e-0938
endocrine gland1.54e-0935
endocrine system1.76e-0945
endo-epithelium2.43e-0982
intestine3.05e-0917
gastrointestinal system4.96e-0925
organ system subdivision1.63e-08223
subdivision of trunk2.26e-08112
immaterial anatomical entity9.11e-08117
segment of respiratory tract3.65e-0747
primordium8.31e-07160
Disease
Ontology termp-valuen
carcinoma1.31e-21106
cell type cancer3.04e-17143
cancer4.03e-10235
disease of cellular proliferation1.05e-09239


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.11.64148
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
MA0046.12.92613
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
MA0060.10.492218
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
MA0081.10.714712
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
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
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.13.156
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
MA0099.20.902716
MA0079.20.00160703
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
CEBPB#105137.971147625824820.001974187055288560.0114864691848068
EP300#203336.77394172622320.003216880500103790.0166716843266346
FOSL2#2355316.93020060456170.0002060162053171620.00242189627049967
FOXA1#3169311.08141974938550.000734755275698670.0057906056624429
FOXA2#3170324.63046375266526.68983856509345e-050.00106995413460918
GTF2F1#2962312.73966087675770.0004835525047438590.00432526036681602
HDAC2#3066313.41562023662630.0004140761399857210.00389671093746339
HNF4A#3172323.13229036295378.07584663437677e-050.00122414128686165
HNF4G#3174328.75342252644684.20470658818262e-050.000754787472264016
JUN#3725312.51282919233630.0005103313992726250.00442862492801277
MAX#414936.452555509007120.003721913834265510.0185587471442757
MXI1#460139.96157162875930.001011470541259020.00717886319120292
MYC#460935.22228187160940.007020843755740150.0292960126655378
NR3C1#2908314.9730233311730.0002978331194675480.00307700001623022
RXRA#6256320.07461713913330.0001235730348432220.00164783505949838
SP1#666735.69838137814090.005403962701712170.0245256588129722
STAT3#6774310.51946499715420.0008589184530415310.00641250870807095
TCF7L2#6934310.77017656313730.0008003181298398380.00611265358800226
TFAP2A#7020316.5186343730450.0002218033880766340.00247197994315821
TFAP2C#7022310.80922860986020.0007916746575753130.00612502478424388
USF1#739136.361499277207960.00388404057290560.0189359216410087
USF2#7392312.99219738506960.0004558979393427810.00420242938102566



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.