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{{Coexpression_clusters
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|full_id=C4826_hepatocellular_Renal_kidney_adenocarcinoma_Intestinal_small_Prostate
|id=C4826
|ontology_enrichment_celltype=CL:0000066!3.31e-19!254;CL:1000507!8.36e-15!12;CL:1000494!8.36e-15!12;CL:1000449!3.61e-14!16;CL:1000497!3.94e-12!18;CL:0002518!3.94e-12!18;CL:0002681!2.77e-10!13;CL:0002584!2.77e-10!13;CL:0000039!2.31e-07!7;CL:0000586!2.31e-07!7;CL:0002322!4.79e-07!5
|ontology_enrichment_disease=DOID:305!1.10e-15!106;DOID:0050687!3.17e-11!143;DOID:299!1.41e-08!25
|ontology_enrichment_uberon=UBERON:0006555!6.11e-15!17;UBERON:0005103!6.11e-15!17;UBERON:0000083!6.11e-15!17;UBERON:0009201!6.11e-15!17;UBERON:0004819!6.11e-15!17;UBERON:0006553!6.11e-15!17;UBERON:0003074!6.11e-15!17;UBERON:0003060!6.11e-15!17;UBERON:0009773!8.36e-15!12;UBERON:0001231!8.36e-15!12;UBERON:0004810!8.36e-15!12;UBERON:0000466!1.03e-14!126;UBERON:0004211!3.61e-14!16;UBERON:0001285!3.61e-14!16;UBERON:0007684!3.61e-14!16;UBERON:0003220!3.61e-14!16;UBERON:0004208!3.61e-14!16;UBERON:0000058!5.04e-14!26;UBERON:0004876!7.15e-14!20;UBERON:0000080!7.39e-14!18;UBERON:0002120!7.39e-14!18;UBERON:0004875!7.39e-14!18;UBERON:0005721!7.39e-14!18;UBERON:0005754!7.39e-14!18;UBERON:0007297!7.39e-14!18;UBERON:0003064!1.95e-13!37;UBERON:0003887!9.74e-13!21;UBERON:0006554!1.04e-12!44;UBERON:0001008!2.94e-12!45;UBERON:0002113!4.41e-12!27;UBERON:0003918!4.41e-12!27;UBERON:0005095!4.41e-12!27;UBERON:0007687!4.41e-12!27;UBERON:0003886!4.73e-12!63;UBERON:0000489!4.96e-12!32;UBERON:0000464!6.28e-12!104;UBERON:0002553!1.05e-11!70;UBERON:0004921!1.17e-11!129;UBERON:0004185!1.17e-11!129;UBERON:0005172!5.55e-11!55;UBERON:0005173!5.55e-11!55;UBERON:0005177!8.99e-11!107;UBERON:0001007!2.54e-10!155;UBERON:0001555!2.54e-10!155;UBERON:0007026!2.54e-10!155;UBERON:0001225!2.77e-10!13;UBERON:0008987!2.77e-10!13;UBERON:0003101!1.44e-09!22;UBERON:0000079!1.44e-09!22;UBERON:0003135!1.99e-09!11;UBERON:0004119!2.62e-09!169;UBERON:0000925!2.62e-09!169;UBERON:0006595!2.62e-09!169;UBERON:0002417!3.85e-09!61;UBERON:0000916!3.85e-09!61;UBERON:0005409!9.37e-09!35;UBERON:0000160!1.45e-08!27;UBERON:0004111!6.97e-08!241;UBERON:0001851!7.75e-08!16;UBERON:0000077!8.79e-08!130;UBERON:0009569!1.21e-07!113;UBERON:0005156!2.54e-07!59;UBERON:0000990!2.54e-07!59;UBERON:0000353!3.21e-07!17;UBERON:0001046!5.40e-07!19
}}

Latest revision as of 14:20, 17 September 2013


Full id: C4826_hepatocellular_Renal_kidney_adenocarcinoma_Intestinal_small_Prostate



Phase1 CAGE Peaks

Hg19::chr9:71735882..71735896,+p6@TJP2
Hg19::chr9:71735910..71735923,+p16@TJP2
Hg19::chr9:71735943..71735948,+p26@TJP2


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
nephron tubule epithelium8.48e-2710
nephron epithelium2.03e-2015
renal tubule2.03e-2015
nephron tubule2.03e-2015
nephron2.03e-2015
uriniferous tubule2.03e-2015
nephrogenic mesenchyme2.03e-2015
excretory tube5.69e-1916
kidney epithelium5.69e-1916
urinary system structure2.42e-1747
renal system7.22e-1748
cavitated compound organ3.90e-1631
kidney3.22e-1526
kidney mesenchyme3.22e-1526
upper urinary tract3.22e-1526
kidney rudiment3.22e-1526
kidney field3.22e-1526
abdomen element4.91e-1554
abdominal segment element4.91e-1554
cortex of kidney1.37e-1312
renal parenchyma1.37e-1312
abdominal segment of trunk5.43e-1360
abdomen5.43e-1360
gastrointestinal system2.15e-1225
trunk region element8.98e-12101
hindgut2.41e-1119
intestine6.40e-1117
cortex1.47e-1015
parenchyma1.47e-1015
subdivision of digestive tract1.80e-10118
male organism1.01e-0922
male reproductive system1.01e-0922
renal cortex tubule1.58e-093
region of nephron tubule1.58e-093
proximal tubule1.58e-093
digestive system1.63e-09145
digestive tract1.63e-09145
primitive gut1.63e-09145
testis3.11e-088
endoderm-derived structure6.34e-08160
endoderm6.34e-08160
presumptive endoderm6.34e-08160
cloaca1.51e-0714
anal region1.51e-0714
embryonic cloaca1.51e-0714
terminal part of digestive tract1.51e-0714
primitive urogenital sinus1.51e-0714
proctodeum1.51e-0714
subdivision of trunk2.04e-07112
gut epithelium3.27e-0754
mesenchyme4.28e-07160
entire embryonic mesenchyme4.28e-07160
genitourinary system5.59e-0715
intermediate mesoderm6.90e-0728
Disease
Ontology termp-valuen
carcinoma3.75e-15106
cell type cancer5.41e-10143
adenocarcinoma6.56e-0925


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
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
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
MA0042.10.810843
MA0043.11.32783
MA0046.12.92613
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.12.75836
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.14.54482
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
MA0101.11.55947
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
MA0131.11.06461
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.22.96208
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.12.94916
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.14.77883
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.10519
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
BCL11A#53335328.36945510360714.37778126761649e-050.00077982448884291
E2F1#186934.907389214879320.008460985347239390.0328252915557331
ELF1#199734.258097958807540.01295179875054610.0465411818644468
ELK4#2005316.2356816584680.0002336043955745990.00256571768528926
EP300#203336.77394172622320.003216880500103790.0168658525376677
FOS#235338.99795530889440.001372499272417130.00902660274004865
FOSL2#2355316.93020060456170.0002060162053171620.00244223909955949
GATA3#2625327.2365163572064.94721007899563e-050.000856000121670352
HDAC2#3066313.41562023662630.0004140761399857210.00394038250423405
HNF4A#3172323.13229036295378.07584663437677e-050.00123579977530795
JUND#372736.994663941871030.002921845042734990.0157824967374295
MYC#460935.22228187160940.007020843755740150.0296490194899416
NANOG#79923329.24477848101273.99627955670032e-050.000742118493282762
NR3C1#2908314.9730233311730.0002978331194675480.00310650086528226
POU5F1#54603335.4392014519062.63510205045339e-081.82498291145426e-06
RXRA#6256320.07461713913330.0001235730348432220.00166141145545717
SIN3A#2594235.408884726815140.006318961977991520.0278622844726613
SP1#666735.69838137814090.005403962701712170.0248179262391327
TAF7#6879311.43306940492390.0006690181981945830.00546298605170008
TCF12#6938310.63446490218640.0008313523990202070.00632563115264981
USF1#739136.361499277207960.00388404057290560.0191378238060808
YY1#752834.911170749853860.008441455341808260.0331597079190248
ZNF263#1012738.221841637010680.001799043925565870.0110277232387706



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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