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{{Coexpression_clusters
{
|full_id=C1761_Placental_Alveolar_Smooth_Fibroblast_mesothelioma_Renal_Urothelial

Latest revision as of 11:51, 17 September 2013


Full id: C1761_Placental_Alveolar_Smooth_Fibroblast_mesothelioma_Renal_Urothelial



Phase1 CAGE Peaks

Hg19::chr16:3070336..3070347,+p2@TNFRSF12A
Hg19::chr16:3070356..3070383,+p1@TNFRSF12A
Hg19::chr16:3071213..3071278,+p@chr16:3071213..3071278
+
Hg19::chr16:3071571..3071641,+p@chr16:3071571..3071641
+
Hg19::chr16:3072067..3072119,-p@chr16:3072067..3072119
-


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><br>

Uber Anatomy
Ontology termp-valuen
organism subdivision4.28e-20264
trunk1.95e-18199
multilaminar epithelium1.08e-1683
epithelial vesicle2.23e-1678
mesenchyme1.36e-15160
entire embryonic mesenchyme1.36e-15160
unilaminar epithelium5.46e-15148
trunk mesenchyme6.13e-15122
somite2.83e-1471
presomitic mesoderm2.83e-1471
presumptive segmental plate2.83e-1471
dermomyotome2.83e-1471
trunk paraxial mesoderm2.83e-1471
epithelial tube3.88e-14117
paraxial mesoderm1.47e-1372
presumptive paraxial mesoderm1.47e-1372
dense mesenchyme tissue1.59e-1373
multi-cellular organism2.17e-12656
skeletal muscle tissue3.33e-1262
striated muscle tissue3.33e-1262
myotome3.33e-1262
anatomical system5.93e-12624
anatomical group8.29e-12625
muscle tissue1.52e-1164
musculature1.52e-1164
musculature of body1.52e-1164
cell layer1.91e-11309
vasculature2.76e-1178
vascular system2.76e-1178
epithelium3.26e-11306
artery5.73e-1142
arterial blood vessel5.73e-1142
arterial system5.73e-1142
splanchnic layer of lateral plate mesoderm1.67e-0983
epithelial tube open at both ends1.69e-0959
blood vessel1.69e-0959
blood vasculature1.69e-0959
vascular cord1.69e-0959
vessel2.50e-0968
systemic artery2.82e-0933
systemic arterial system2.82e-0933
multi-tissue structure5.32e-09342
urinary system structure2.70e-0847
primordium3.50e-08160
renal system7.64e-0848
embryo1.26e-07592
developing anatomical structure1.29e-07581
subdivision of trunk2.53e-07112
nephron epithelium2.62e-0715
renal tubule2.62e-0715
nephron tubule2.62e-0715
nephron2.62e-0715
uriniferous tubule2.62e-0715
nephrogenic mesenchyme2.62e-0715
ectodermal placode2.96e-0731
surface structure3.88e-0799
female organism5.01e-0741
excretory tube9.59e-0716
kidney epithelium9.59e-0716


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)
MA0003.13.78382
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.45664
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.28241
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.16.09397
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.58771
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.21.41923
MA0035.20.691506
MA0039.23.98195
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.23.37937
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.11.3196
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.27.74761
MA0102.21.66336
MA0258.12.47453
MA0259.11.02361
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#90545.068961261570110.002709998091280770.0148955050079087
EGR1#195843.990543275848110.0067800983001440.0287661149808555
ESR1#2099212.30744131846180.009891532076757460.0371177679852139
ETS1#211347.783008737761870.0005121035947688870.00444031443205212
FOSL1#8061215.88543188654920.006026021505811330.0270050057946977
GABPB1#255345.654147068945740.001776696502096670.0109080245713053
JUNB#3726212.24425306392850.009990490593345960.0374689139612331
SMARCC1#6599326.19801559177890.0001159625626060410.00157633920031398
TAF1#687253.343046285745290.002394600090870310.0135315246667246
ZBTB7A#5134145.881527446300720.001524947561042230.00971477359568683



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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