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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.489875373956975,

Latest revision as of 12:14, 17 September 2013


Full id: C2879_salivary_Fibroblast_vagina_liver_Hepatocyte_Skeletal_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr7:134576184..134576236,+p2@CALD1
Hg19::chr7:134576237..134576280,+p5@CALD1
Hg19::chr7:134576283..134576309,+p9@CALD1
Hg19::chr7:134576317..134576374,+p3@CALD1


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.41e-25342
organ system subdivision3.91e-17223
anatomical cluster6.39e-17373
multi-cellular organism8.08e-16656
endoderm-derived structure3.10e-15160
endoderm3.10e-15160
presumptive endoderm3.10e-15160
organism subdivision6.09e-14264
anatomical system1.61e-13624
anatomical group3.11e-13625
cell layer3.72e-13309
digestive system6.90e-13145
digestive tract6.90e-13145
primitive gut6.90e-13145
epithelium1.17e-12306
organ4.62e-12503
ectoderm-derived structure8.96e-12171
ectoderm8.96e-12171
presumptive ectoderm8.96e-12171
surface structure9.82e-1299
mesenchyme1.09e-11160
entire embryonic mesenchyme1.09e-11160
embryo3.12e-11592
developing anatomical structure1.79e-10581
organ part1.03e-09218
primordium1.33e-09160
subdivision of digestive tract1.38e-09118
embryonic structure1.52e-09564
trunk2.73e-09199
trunk mesenchyme3.41e-09122
germ layer6.00e-09560
germ layer / neural crest6.00e-09560
embryonic tissue6.00e-09560
presumptive structure6.00e-09560
germ layer / neural crest derived structure6.00e-09560
epiblast (generic)6.00e-09560
gland1.43e-0859
adult organism2.61e-08114
structure with developmental contribution from neural crest2.64e-08132
orifice7.74e-0836
organ component layer7.79e-0766
exocrine gland7.90e-0731
exocrine system7.90e-0731
ecto-epithelium8.55e-07104


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
MA0006.10.532262
MA0007.10.6918
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
MA0041.12.91216
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
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.12.63476
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.12.01886
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.13.3942
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
MA0145.11.70272
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.476674
MA0102.21.75932
MA0258.11.07498
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
CEBPB#105147.971147625824820.0002476385788090830.00268651973950782
EP300#203346.77394172622320.0004748459821442640.00435288681902614
FOXA1#3169411.08141974938556.62943068949433e-050.00107344358415519
FOXA2#3170424.63046375266522.71504128667089e-069.4550249062561e-05
GATA2#2624412.7449317335543.78864877853583e-050.000724428212708722
GTF2F1#2962412.73966087675773.79492332235515e-050.000719306709371053
HDAC2#3066413.41562023662633.0859005065161e-050.000628610031207402
HEY1#2346244.040111043105710.00375304636917980.01866052890982
MAX#414946.452555509007120.0005767613195645490.00486522699733478
MXI1#460149.96157162875930.0001015224754950450.00142761624050451
MYC#460945.22228187160940.001344309395272740.00889892431595927
NR3C1#2908414.9730233311731.98868032687801e-050.000444649506869647
RAD21#5885410.35503389545638.6948481184721e-050.00129930067627001
RFX5#5993412.04791082719514.74457429336527e-050.000828626412416012
SMARCB1#6598418.25271578115749.00423392720929e-060.000242182123905179
SP1#666745.69838137814090.0009482606065333980.00685698189335606
TAF1#687243.343046285745290.008005664898701650.0323319271599189
TBP#690843.706770687096390.005296377814784350.0245016124467693
TCF7L2#6934410.77017656313737.42969445082454e-050.00115761578211199
TRIM28#10155418.59052504526258.36730015875654e-060.000231060936351236
USF1#739146.361499277207960.0006105011399140830.00509062902606682
USF2#7392412.99219738506963.50833029870167e-050.000683084466939044
YY1#752844.911170749853860.00171871838055440.0107088192904618
ZNF263#1012748.221841637010680.0002187871180958320.00249944299133785



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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