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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 12:03, 17 September 2013


Full id: C2343_squamous_malignant_meningioma_embryonic_mesothelioma_bile_papillotubular



Phase1 CAGE Peaks

Hg19::chr15:67418047..67418093,+p4@SMAD3
Hg19::chr15:67418099..67418118,+p16@SMAD3
Hg19::chr15:67418119..67418162,+p5@SMAD3
Hg19::chr15:67418177..67418204,+p9@SMAD3


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>

Uber Anatomy
Ontology termp-valuen
organism subdivision2.50e-18264
multi-tissue structure2.99e-15342
epithelial tube1.95e-13117
cell layer2.73e-13309
multilaminar epithelium3.32e-1383
epithelium8.95e-13306
artery2.76e-1242
arterial blood vessel2.76e-1242
arterial system2.76e-1242
vasculature1.19e-1178
vascular system1.19e-1178
unilaminar epithelium1.69e-11148
skeletal muscle tissue1.91e-1162
striated muscle tissue1.91e-1162
myotome1.91e-1162
trunk mesenchyme2.43e-11122
anatomical cluster3.28e-11373
systemic artery4.49e-1133
systemic arterial system4.49e-1133
muscle tissue4.94e-1164
musculature4.94e-1164
musculature of body4.94e-1164
epithelial vesicle7.78e-1178
trunk8.42e-11199
epithelial tube open at both ends1.21e-1059
blood vessel1.21e-1059
blood vasculature1.21e-1059
vascular cord1.21e-1059
somite2.92e-1071
presomitic mesoderm2.92e-1071
presumptive segmental plate2.92e-1071
dermomyotome2.92e-1071
trunk paraxial mesoderm2.92e-1071
vessel3.13e-1068
dense mesenchyme tissue3.16e-1073
paraxial mesoderm4.34e-1072
presumptive paraxial mesoderm4.34e-1072
endoderm-derived structure4.54e-10160
endoderm4.54e-10160
presumptive endoderm4.54e-10160
splanchnic layer of lateral plate mesoderm5.37e-1083
primordium1.86e-09160
mesenchyme3.17e-09160
entire embryonic mesenchyme3.17e-09160
digestive system5.94e-09145
digestive tract5.94e-09145
primitive gut5.94e-09145
respiratory system6.95e-0974
anatomical system1.04e-08624
anatomical conduit1.07e-08240
anatomical group1.63e-08625
head2.27e-0856
surface structure4.96e-0899
anterior region of body5.53e-0862
craniocervical region5.53e-0862
cardiovascular system8.39e-08109
circulatory system1.34e-07112
subdivision of head1.54e-0749
respiratory tract3.86e-0754
segment of respiratory tract4.28e-0747
multi-cellular organism5.76e-07656
Disease
Ontology termp-valuen
carcinoma3.56e-08106
squamous cell carcinoma5.16e-0714


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.12.49947
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.14.05751
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
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
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
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
MA0116.11.15856
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
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.21.99204
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.23.08317
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BRCA1#672420.18423064322386.02116732184487e-060.000179362434091887
CEBPB#105147.971147625824820.0002476385788090830.00267789661754419
E2F1#186944.907389214879320.001724022357361790.0106403008498114
EP300#203346.77394172622320.0004748459821442640.00433765761647554
ESR1#2099430.76860329615451.11467714392546e-064.59959566315412e-05
FOS#235348.99795530889440.0001525147711168630.00194701016754358
FOSL1#8061439.7135797163734.01511434669553e-071.93688003350824e-05
FOXA1#3169411.08141974938556.62943068949433e-050.00106946418254572
GATA2#2624412.7449317335543.78864877853583e-050.000720996154849679
GATA3#2625427.2365163572061.81561517799785e-066.76251902906266e-05
JUN#3725412.51282919233634.07770316866756e-050.000742065239993851
JUNB#3726430.61063265982111.13787152942193e-064.65120018243825e-05
JUND#372746.994663941871030.000417684217818580.00391198296338935
MAX#414946.452555509007120.0005767613195645490.00485034024108237
MXI1#460149.96157162875930.0001015224754950450.00142206354858194
MYC#460945.22228187160940.001344309395272740.00886800965973278
NR3C1#2908414.9730233311731.98868032687801e-050.000442282335304115
RAD21#5885410.35503389545638.6948481184721e-050.00129190673302761
RFX5#5993412.04791082719514.74457429336527e-050.000826001991373188
SMARCB1#6598418.25271578115749.00423392720929e-060.00024106464678898
SMC3#9126415.04493284493281.95092670935632e-050.000437237842485976
STAT1#6772420.70658749719925.43610708103893e-060.000165137169120601
STAT3#6774410.51946499715428.16377768286615e-050.00123014972936208
TAF1#687243.343046285745290.008005664898701650.0321788721993419
TBP#690843.706770687096390.005296377814784350.0243860337079867
TCF7L2#6934410.77017656313737.42969445082454e-050.00115245783268924
TFAP2A#7020416.5186343730451.34240829060362e-050.000326349579754077
TFAP2C#7022410.80922860986027.32289634782688e-050.00114456146613393
ZBTB7A#5134147.35190930787590.000342223540015990.00346198026886187



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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