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{{Coexpression_clusters
{
|full_id=C2216_keratoacanthoma_cervical_synovial_Wilms_gastric_oral_mesothelioma
 

Latest revision as of 12:01, 17 September 2013


Full id: C2216_keratoacanthoma_cervical_synovial_Wilms_gastric_oral_mesothelioma



Phase1 CAGE Peaks

Hg19::chr12:54332608..54332636,+p1@HOXC13
Hg19::chr12:54332652..54332671,+p2@HOXC13
Hg19::chr12:54332675..54332686,+p4@HOXC13
Hg19::chr12:54332687..54332701,+p3@HOXC13


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
epithelial cell1.64e-19253
squamous epithelial cell1.63e-1363
mammary gland epithelial cell7.78e-084
mesothelial cell4.99e-0719
epithelial cell of alimentary canal9.20e-0720
Uber Anatomy
Ontology termp-valuen
larynx7.82e-169
breast3.16e-0910
chest3.04e-0811
upper respiratory tract5.87e-0819
mammary gland7.78e-084
mammary bud7.78e-084
mammary ridge7.78e-084
mammary placode7.78e-084
mucosa of oral region1.28e-074
respiratory system mucosa1.28e-074
Disease
Ontology termp-valuen
cell type cancer3.54e-39143
cancer4.74e-35235
disease of cellular proliferation8.57e-34239
carcinoma8.05e-30106
squamous cell carcinoma2.20e-1814
thoracic cancer2.08e-074
breast cancer2.08e-074


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
MA0004.15.48953
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.18.81203
MA0058.17.62927
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.12.31526
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.12.31225
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.18.44346
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.12.05499
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
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
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.23.07509
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.22.6968
MA0047.20.856092
MA0112.20.187982
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.210.6102
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
ATF3#467422.46317452600873.92475754624726e-060.000127139501666414
CCNT2#90546.336201576962630.0006203100587215640.0051148399039019
CEBPB#105147.971147625824820.0002476385788090830.0026762340161674
E2F1#186944.907389214879320.001724022357361790.0106308774269651
E2F6#187645.017155731697390.00157802193473060.00995451998316797
EGR1#195844.988179094810140.001615011500076050.0101309499703552
FOS#235348.99795530889440.0001525147711168630.0019458209358263
GATA3#2625427.2365163572061.81561517799785e-066.75288581107254e-05
IRF1#365947.63716375356390.0002938853996185490.00306930972507616
MAX#414946.452555509007120.0005767613195645490.00484682776424219
MXI1#460149.96157162875930.0001015224754950450.00142149159649108
NFE2#4778477.2042606516292.80776035215453e-081.91534737699978e-06
NFYB#4801416.75979325353651.26678572070404e-050.000311078847600774
NRF1#4899412.21027944771094.49717228915276e-050.000792441668140417
RAD21#5885410.35503389545638.6948481184721e-050.00129117196451743
SMARCB1#6598418.25271578115749.00423392720929e-060.000240817717573319
SMARCC2#6601494.15537442689761.26854362961227e-089.39612965482805e-07
SP1#666745.69838137814090.0009482606065333980.00683191152633427
TBP#690843.706770687096390.005296377814784350.0243613319210016
TFAP2A#7020416.5186343730451.34240829060362e-050.000326045998749654
TFAP2C#7022410.80922860986027.32289634782688e-050.00114387671503244
THAP1#55145431.36914460285131.03171810326891e-064.31006427949207e-05
USF1#739146.361499277207960.0006105011399140830.00507119450819112
USF2#7392412.99219738506963.50833029870167e-050.000680168012003162



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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