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Coexpression cluster:C3708: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3708_stomach_colon_hepatoblastoma_ovary_heart_Hepatic_mesothelioma
|id=C3708
}}

Latest revision as of 12:31, 17 September 2013


Full id: C3708_stomach_colon_hepatoblastoma_ovary_heart_Hepatic_mesothelioma



Phase1 CAGE Peaks

Hg19::chr18:19749504..19749515,+p5@GATA6
Hg19::chr18:19749517..19749531,+p3@GATA6
Hg19::chr18:19749541..19749557,+p1@GATA6


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
mesodermal cell2.06e-09121
smooth muscle cell9.56e-0943
smooth muscle myoblast9.56e-0943
epithelial cell1.23e-08253
embryonic cell3.53e-08250
muscle cell7.73e-0855
contractile cell8.63e-0859
vascular associated smooth muscle cell1.25e-0732
cardiocyte2.84e-0716
muscle precursor cell6.91e-0758
myoblast6.91e-0758
multi-potent skeletal muscle stem cell6.91e-0758
Uber Anatomy
Ontology termp-valuen
epithelial tube1.54e-26117
trunk3.88e-20199
splanchnic layer of lateral plate mesoderm5.89e-1983
unilaminar epithelium2.58e-15148
immaterial anatomical entity3.67e-15117
mesenchyme4.06e-15160
entire embryonic mesenchyme4.06e-15160
trunk mesenchyme3.57e-14122
primordium4.22e-14160
circulatory system4.63e-14112
subdivision of digestive tract9.88e-14118
primary circulatory organ2.44e-1327
organism subdivision2.86e-13264
epithelial tube open at both ends3.19e-1359
blood vessel3.19e-1359
blood vasculature3.19e-1359
vascular cord3.19e-1359
cardiovascular system1.03e-12109
subdivision of trunk2.96e-12112
anatomical cluster6.27e-12373
artery1.05e-1142
arterial blood vessel1.05e-1142
arterial system1.05e-1142
endoderm-derived structure1.41e-11160
endoderm1.41e-11160
presumptive endoderm1.41e-11160
vasculature1.69e-1178
vascular system1.69e-1178
heart1.73e-1124
primitive heart tube1.73e-1124
primary heart field1.73e-1124
anterior lateral plate mesoderm1.73e-1124
heart tube1.73e-1124
heart primordium1.73e-1124
cardiac mesoderm1.73e-1124
cardiogenic plate1.73e-1124
heart rudiment1.73e-1124
digestive system4.77e-11145
digestive tract4.77e-11145
primitive gut4.77e-11145
compound organ3.41e-1068
vessel3.50e-1068
trunk region element5.63e-10101
body cavity precursor8.62e-1054
multi-tissue structure9.20e-10342
endo-epithelium9.23e-1082
gut epithelium1.38e-0954
body cavity or lining1.74e-0949
anatomical space1.90e-0995
body cavity8.13e-0946
cell layer8.29e-09309
systemic artery1.11e-0833
systemic arterial system1.11e-0833
tube1.27e-08192
epithelium1.33e-08306
epithelial sac1.77e-0825
anatomical conduit1.83e-08240
epithelium of foregut-midgut junction2.29e-0825
anatomical boundary2.29e-0825
hepatobiliary system2.29e-0825
foregut-midgut junction2.29e-0825
septum transversum2.29e-0825
sac2.35e-0826
reproductive structure5.98e-0859
reproductive system5.98e-0859
anatomical cavity8.85e-0861
hepatic diverticulum9.54e-0822
liver primordium9.54e-0822
digestive tract diverticulum1.28e-0723
muscle tissue1.58e-0764
musculature1.58e-0764
musculature of body1.58e-0764
abdominal segment of trunk2.03e-0760
abdomen2.03e-0760
foregut6.03e-0787
liver6.94e-0719
digestive gland6.94e-0719
liver bud6.94e-0719
gastrointestinal system8.79e-0725
Disease
Ontology termp-valuen
cell type cancer4.59e-08143
carcinoma8.61e-08106


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.11.89908
MA0043.11.32783
MA0046.11.31611
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
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
MA0078.12.37746
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0131.12.4174
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
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.21.20011
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
MA0154.10.838867
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.25.16052
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
CTBP2#1488362.71700033932814.049570681927e-060.000129614806144583
CTCF#1066435.360256373075030.0064925092527670.0279259986759085
E2F1#186934.907389214879320.008460985347239390.0325077014560694
E2F6#187635.017155731697390.00791769806886330.0321920219805354
EGR1#195834.988179094810140.008056488137383440.0320427877900982
FOXA1#3169311.08141974938550.000734755275698670.00580945614646781
FOXA2#3170324.63046375266526.68983856509345e-050.00107192397959465
RAD21#5885310.35503389545630.0009004912073565420.00663700784792589
SMC3#9126315.04493284493280.0002935825420371870.00308900535037495
ZBTB7A#5134137.35190930787590.002516255860282270.0140090221116275
ZNF263#1012738.221841637010680.001799043925565870.010934028662836



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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