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{{Coexpression_clusters
{
|full_id=C316_hepatic_Hair_Fibroblast_spindle_Preadipocyte_tenocyte_Ewing
 

Latest revision as of 11:20, 17 September 2013


Full id: C316_hepatic_Hair_Fibroblast_spindle_Preadipocyte_tenocyte_Ewing



Phase1 CAGE Peaks

Hg19::chr15:33010194..33010211,+p1@GREM1
Hg19::chr15:33010431..33010449,+p@chr15:33010431..33010449
+
Hg19::chr15:33022885..33022907,+p12@GREM1
Hg19::chr15:33022910..33022924,+p13@GREM1
Hg19::chr15:33022957..33022966,-p14@CU686887
Hg19::chr15:33022972..33022997,+p3@GREM1
Hg19::chr15:33023020..33023043,-p2@CU686887
Hg19::chr15:33023069..33023091,+p5@GREM1
Hg19::chr15:33023095..33023177,+p2@GREM1
Hg19::chr15:33023166..33023177,-p12@CU686887
Hg19::chr15:33023180..33023193,+p15@GREM1
Hg19::chr15:33023199..33023239,+p7@GREM1
Hg19::chr15:33023250..33023262,+p19@GREM1
Hg19::chr15:33023284..33023311,-p4@CU686887
Hg19::chr15:33023286..33023299,+p4@GREM1
Hg19::chr15:33023302..33023311,+p27@GREM1
Hg19::chr15:33023323..33023333,+p20@GREM1
Hg19::chr15:33023369..33023426,-p1@CU686887
Hg19::chr15:33023489..33023500,-p8@CU686887
Hg19::chr15:33023541..33023550,-p10@CU686887
Hg19::chr15:33023745..33023757,+p11@GREM1
Hg19::chr15:33023840..33023851,+p14@GREM1
Hg19::chr15:33023873..33023883,+p22@GREM1
Hg19::chr15:33024106..33024122,+p9@GREM1
Hg19::chr15:33024150..33024170,-p@chr15:33024150..33024170
-
Hg19::chr15:33024167..33024179,+p18@GREM1
Hg19::chr15:33024232..33024264,-p@chr15:33024232..33024264
-
Hg19::chr15:33024456..33024470,+p6@GREM1
Hg19::chr15:33024736..33024758,+p10@GREM1
Hg19::chr15:33024771..33024780,+p24@GREM1
Hg19::chr15:33024966..33024984,+p21@GREM1
Hg19::chr15:33024989..33024999,+p17@GREM1
Hg19::chr15:33025032..33025060,+p8@GREM1
Hg19::chr15:33025271..33025279,+p@chr15:33025271..33025279
+
Hg19::chr15:33025543..33025554,+p@chr15:33025543..33025554
+
Hg19::chr15:33025787..33025805,+p@chr15:33025787..33025805
+
Hg19::chr15:33026325..33026338,+p@chr15:33026325..33026338
+
Hg19::chr17:30745..30746,-p@chr17:30745..30746
-


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
fibroblast5.83e-3076
multi fate stem cell7.59e-20427
skin fibroblast7.97e-2023
somatic stem cell4.28e-19433
stem cell3.97e-18441
preadipocyte4.19e-1612
connective tissue cell1.53e-13361
somatic cell3.05e-13588
mesenchymal cell3.00e-12354
motile cell2.57e-10386
muscle precursor cell1.07e-0858
myoblast1.07e-0858
multi-potent skeletal muscle stem cell1.07e-0858
animal cell1.92e-08679
eukaryotic cell1.92e-08679
stromal cell2.37e-0828
smooth muscle cell6.69e-0843
smooth muscle myoblast6.69e-0843
muscle cell6.89e-0755
Uber Anatomy
Ontology termp-valuen
integument3.21e-1546
integumental system3.21e-1546
skin of body4.86e-1541
connective tissue1.24e-13371
surface structure9.07e-1299
dense mesenchyme tissue1.38e-1173
somite4.07e-1171
presomitic mesoderm4.07e-1171
presumptive segmental plate4.07e-1171
dermomyotome4.07e-1171
trunk paraxial mesoderm4.07e-1171
paraxial mesoderm7.80e-1172
presumptive paraxial mesoderm7.80e-1172
multilaminar epithelium1.93e-1083
epithelial vesicle4.78e-1078
omentum3.34e-096
peritoneum3.34e-096
abdominal cavity3.34e-096
visceral peritoneum3.34e-096
trunk mesenchyme2.23e-08122
cavity lining2.63e-0812
serous membrane2.63e-0812
body cavity or lining3.31e-0849
female gonad3.56e-0813
skeletal muscle tissue1.08e-0762
striated muscle tissue1.08e-0762
myotome1.08e-0762
organ component layer2.99e-0766
muscle tissue3.03e-0764
musculature3.03e-0764
musculature of body3.03e-0764
right ovary5.73e-075
Disease
Ontology termp-valuen
ovarian cancer2.36e-1114
musculoskeletal system disease3.02e-085
myotonic disease3.02e-085
muscle tissue disease3.02e-085
myopathy3.02e-085
muscular disease3.02e-085
myotonic dystrophy3.02e-085


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)
MA0003.10.00945289
MA0004.10.473448
MA0006.10.0748843
MA0007.10.0532455
MA0009.13.3705
MA0014.10.345302
MA0017.10.474929
MA0019.13.26955
MA0024.10.261871
MA0025.10.448136
MA0027.11.8578
MA0028.10.680836
MA0029.10.275814
MA0030.10.267514
MA0031.11.84835
MA0038.10.104656
MA0040.10.280083
MA0041.10.0671563
MA0042.10.0551182
MA0043.10.34048
MA0046.10.331797
MA0048.10.107905
MA0050.10.203478
MA0051.12.27201
MA0052.10.282917
MA0055.10.00437922
MA0056.10
MA0057.10.0201404
MA0058.10.0300567
MA0059.10.0297304
MA0060.10.0191619
MA0061.10.514722
MA0063.10
MA0066.10.341748
MA0067.10.607707
MA0068.10.965797
MA0069.10.876534
MA0070.13.24562
MA0071.10.0863631
MA0072.10.31681
MA0073.15.50559e-06
MA0074.11.13272
MA0076.10.322093
MA0077.10.310955
MA0078.11.47491
MA0081.10.0297714
MA0083.10.346089
MA0084.10.778769
MA0087.10.314949
MA0088.10.163236
MA0089.10
MA0090.11.39676
MA0091.10.0609953
MA0092.10.403964
MA0093.10.384002
MA0095.10
MA0098.10
MA0100.15.4267
MA0101.10.202326
MA0103.10.180166
MA0105.10.0755329
MA0106.111.6479
MA0107.10.22925
MA0108.20.628203
MA0109.10
MA0111.10.0424161
MA0113.10.419724
MA0114.13.90636
MA0115.10.540206
MA0116.10.64523
MA0117.10.369828
MA0119.10.495524
MA0122.10.390603
MA0124.10.504249
MA0125.10.433225
MA0130.10
MA0131.10.16707
MA0132.10
MA0133.10
MA0135.10.954806
MA0136.10.71182
MA0139.10.00974208
MA0140.10.602871
MA0141.10.849021
MA0142.10.201309
MA0143.10.134991
MA0144.10.0296118
MA0145.12.3084
MA0146.10.000189556
MA0147.10.116066
MA0148.11.34882
MA0149.10.0808931
MA0062.20.70353
MA0035.20.0848533
MA0039.20.662802
MA0138.20.156943
MA0002.20.5878
MA0137.20.226541
MA0104.20.018939
MA0047.20.119486
MA0112.20.00126824
MA0065.21.22147
MA0150.10.95563
MA0151.10
MA0152.11.03439
MA0153.12.8228
MA0154.10.464986
MA0155.10.635865
MA0156.10.712454
MA0157.12.32409
MA0158.10
MA0159.16.58062
MA0160.10.0759929
MA0161.10
MA0162.10.0680779
MA0163.11.4015
MA0164.10.860729
MA0080.20.38421
MA0018.20.126682
MA0099.21.53507
MA0079.26.13748e-05
MA0102.20.813509
MA0258.10.0794293
MA0259.10.00877325
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
EGR1#1958141.837750192824790.0122758854700140.0444935347077144
JUND#3727152.761051556001720.0001234077415888710.0016598301511655
TCF12#6938102.798543395312220.002156190124505460.0124442053720836
USF1#7391132.176302384307990.003949943394630670.0189633234435889



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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