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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 12:23, 17 September 2013


Full id: C3291_large_Fibroblast_Mesenchymal_anaplastic_Renal_cervical_Pericytes



Phase1 CAGE Peaks

Hg19::chr12:53343573..53343584,-p6@KRT8
Hg19::chr12:53343602..53343631,-p3@KRT8
Hg19::chr12:53343633..53343696,-p2@KRT8


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
epithelial tube4.91e-22117
organism subdivision2.43e-18264
trunk5.75e-18199
unilaminar epithelium6.11e-18148
vasculature8.49e-1778
vascular system8.49e-1778
primordium7.74e-15160
anatomical cluster8.08e-15373
mesenchyme4.69e-14160
entire embryonic mesenchyme4.69e-14160
trunk region element3.14e-13101
splanchnic layer of lateral plate mesoderm5.57e-1383
immaterial anatomical entity5.96e-13117
endoderm-derived structure1.15e-12160
endoderm1.15e-12160
presumptive endoderm1.15e-12160
cardiovascular system2.71e-12109
cell layer2.95e-12309
vessel3.26e-1268
epithelium1.44e-11306
trunk mesenchyme2.93e-11122
circulatory system3.55e-11112
multi-tissue structure9.13e-11342
epithelial tube open at both ends1.26e-1059
blood vessel1.26e-1059
blood vasculature1.26e-1059
vascular cord1.26e-1059
subdivision of trunk1.35e-10112
endo-epithelium2.01e-1082
subdivision of digestive tract2.24e-10118
digestive system4.29e-10145
digestive tract4.29e-10145
primitive gut4.29e-10145
urinary system structure1.57e-0947
simple squamous epithelium1.85e-0922
renal system2.71e-0948
anatomical space3.97e-0995
anatomical conduit4.31e-09240
blood vessel endothelium1.80e-0818
endothelium1.80e-0818
cardiovascular system endothelium1.80e-0818
foregut2.80e-0887
abdomen element4.59e-0854
abdominal segment element4.59e-0854
abdominal segment of trunk1.03e-0760
abdomen1.03e-0760
artery3.25e-0742
arterial blood vessel3.25e-0742
arterial system3.25e-0742
gut epithelium5.30e-0754
squamous epithelium5.36e-0725
Disease
Ontology termp-valuen
carcinoma5.24e-12106
cell type cancer8.84e-10143
disease of cellular proliferation7.50e-09239
cancer8.81e-09235


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.12.74347
MA0031.12.60497
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
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
MA0078.11.04495
MA0081.11.70054
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
MA0131.11.06461
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
MA0144.12.26598
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.13.38595
MA0062.21.141
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.760954
MA0150.12.94916
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.22.08754
MA0079.20.941469
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
CCNT2#90536.336201576962630.003930750035764890.0189443287025957
CHD2#1106310.34402283411690.0009033701102746880.00658986316595503
CTCF#1066435.360256373075030.0064925092527670.0278663203817751
ELF1#199734.258097958807540.01295179875054610.0460609837473451
ELK4#2005316.2356816584680.0002336043955745990.00255229725592798
EP300#203336.77394172622320.003216880500103790.0167031809958407
ETS1#211339.728760922202340.001085840092584840.0076064158179266
FOS#235338.99795530889440.001372499272417130.00895386666949669
FOSL1#8061339.7135797163731.59554825631833e-050.000370387784711337
FOSL2#2355316.93020060456170.0002060162053171620.00242489873403799
FOXA1#3169311.08141974938550.000734755275698670.0057993580893813
FOXA2#3170324.63046375266526.68983856509345e-050.00107077402283494
GABPB1#255337.067683836182170.002832212825417420.0153722833007884
GATA2#2624312.7449317335540.0004829527704283790.00436248956848032
GTF2F1#2962312.73966087675770.0004835525047438590.00432971022316049
HDAC2#3066313.41562023662630.0004140761399857210.00390163280259552
HNF4A#3172323.13229036295378.07584663437677e-050.00122556429329799
IRF1#365937.63716375356390.002244692747297240.0127749695294522
JUN#3725312.51282919233630.0005103313992726250.00443341382537296
JUNB#3726330.61063265982113.4847716247536e-050.000679637840742561
JUND#372736.994663941871030.002921845042734990.0156313172020387
MAFK#7975327.10073313782995.02195559325033e-050.00085630697176077
MAX#414936.452555509007120.003721913834265510.0186022664116029
MXI1#460139.96157162875930.001011470541259020.0071891228976828
MYC#460935.22228187160940.007020843755740150.0293523037911111
RAD21#5885310.35503389545630.0009004912073565420.00662438551842712
REST#597839.650028716128020.001112636247114590.00765901773084634
RFX5#5993312.04791082719510.0005717246050312580.00483484583197243
RXRA#6256320.07461713913330.0001235730348432220.00164909841374793
SMARCA4#65973156.7659033078882.58908533335753e-071.33928421560439e-05
SMARCB1#6598318.25271578115740.000164397760679890.00202662154481197
SMC3#9126315.04493284493280.0002935825420371870.00308372393722435
SP1#666735.69838137814090.005403962701712170.0245683641217185
SPI1#668838.204323508522730.001810593189410520.0108895215726372
TAF7#6879311.43306940492390.0006690181981945830.00541262619887242
TFAP2A#7020316.5186343730450.0002218033880766340.00247594314315258
TFAP2C#7022310.80922860986020.0007916746575753130.00613821154881278
TRIM28#10155318.59052504526250.0001555969297255280.00196640703577013
YY1#752834.911170749853860.008441455341808260.0328324577105286
ZNF263#1012738.221841637010680.001799043925565870.0109035717584827



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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