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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:19, 17 September 2013


Full id: C305_heart_skeletal_smooth_left_bladder_penis_esophagus



Phase1 CAGE Peaks

Hg19::chr19:4518464..4518482,-p@chr19:4518464..4518482
-
Hg19::chr22:31489256..31489265,+p16@SMTN
Hg19::chr2:220283091..220283108,+p1@DES
Hg19::chr2:220284823..220284842,+p4@DES
Hg19::chr2:220284844..220284884,-p@chr2:220284844..220284884
-
Hg19::chr2:220284966..220284986,+p5@DES
Hg19::chr2:220284988..220285027,+p6@DES
Hg19::chr2:220285210..220285239,+p@chr2:220285210..220285239
+
Hg19::chr2:220285256..220285296,+p@chr2:220285256..220285296
+
Hg19::chr2:220285302..220285343,+p@chr2:220285302..220285343
+
Hg19::chr2:220285541..220285559,+p@chr2:220285541..220285559
+
Hg19::chr2:220285575..220285610,-p@chr2:220285575..220285610
-
Hg19::chr2:220285599..220285647,+p@chr2:220285599..220285647
+
Hg19::chr2:220285612..220285644,-p@chr2:220285612..220285644
-
Hg19::chr2:220285651..220285664,-p@chr2:220285651..220285664
-
Hg19::chr2:220286055..220286065,+p@chr2:220286055..220286065
+
Hg19::chr2:220286085..220286098,+p@chr2:220286085..220286098
+
Hg19::chr2:220286112..220286136,+p@chr2:220286112..220286136
+
Hg19::chr2:220286147..220286161,+p@chr2:220286147..220286161
+
Hg19::chr2:220286168..220286188,+p@chr2:220286168..220286188
+
Hg19::chr2:220286193..220286205,+p@chr2:220286193..220286205
+
Hg19::chr2:220290377..220290387,+p13@DES
Hg19::chr2:220290396..220290425,+p3@DES
Hg19::chr2:220290408..220290419,-p@chr2:220290408..220290419
-
Hg19::chr2:220290421..220290473,-p@chr2:220290421..220290473
-
Hg19::chr2:220290664..220290727,+p@chr2:220290664..220290727
+
Hg19::chr2:220290729..220290776,+p@chr2:220290729..220290776
+
Hg19::chr2:220290781..220290803,+p@chr2:220290781..220290803
+
Hg19::chr2:220290804..220290823,+p@chr2:220290804..220290823
+
Hg19::chr2:220290830..220290837,+p@chr2:220290830..220290837
+
Hg19::chr2:220290845..220290851,+p@chr2:220290845..220290851
+
Hg19::chr2:220290992..220291014,+p@chr2:220290992..220291014
+
Hg19::chr2:220291020..220291028,+p@chr2:220291020..220291028
+
Hg19::chr2:220291067..220291084,+p@chr2:220291067..220291084
+
Hg19::chr2:220291089..220291100,+p@chr2:220291089..220291100
+
Hg19::chr2:220291155..220291166,+p@chr2:220291155..220291166
+
Hg19::chr2:220291179..220291201,+p@chr2:220291179..220291201
+
Hg19::chr2:220291235..220291266,+p@chr2:220291235..220291266
+
Hg19::chr2:220291318..220291369,-p1@ENST00000431827
Hg19::chr2:220291449..220291458,-p@chr2:220291449..220291458
-


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

GO IDGO nameFDR corrected p-value
GO:0003012muscle system process0.000644808923970424
GO:0006936muscle contraction0.000644808923970424
GO:0045098type III intermediate filament0.00215860867718525
GO:0030018Z disc0.00917206142502409
GO:0042383sarcolemma0.00917206142502409
GO:0031674I band0.00917206142502409
GO:0005626insoluble fraction0.00924872907672752
GO:0005856cytoskeleton0.0103543064344058
GO:0003008system process0.0103543064344058
GO:0006939smooth muscle contraction0.0103543064344058
GO:0008016regulation of heart contraction0.0103543064344058
GO:0008307structural constituent of muscle0.0103543064344058
GO:0003015heart process0.0103543064344058
GO:0060047heart contraction0.0103543064344058
GO:0030017sarcomere0.0103543064344058
GO:0030016myofibril0.0107175356890367
GO:0044449contractile fiber part0.0114181724757752
GO:0043292contractile fiber0.0115020737324959
GO:0005200structural constituent of cytoskeleton0.014467704270575
GO:0043232intracellular non-membrane-bound organelle0.0193433145647536
GO:0043228non-membrane-bound organelle0.0193433145647536
GO:0008015blood circulation0.0224722302354123
GO:0003013circulatory system process0.0224722302354123
GO:0007517muscle development0.0231469802933627
GO:0032501multicellular organismal process0.0278394694516853
GO:0045111intermediate filament cytoskeleton0.0282042822928545
GO:0005882intermediate filament0.0282042822928545
GO:0051239regulation of multicellular organismal process0.0319025563823224
GO:0015629actin cytoskeleton0.0329060306007821
GO:0003779actin binding0.046970160060924



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
cell of skeletal muscle5.82e-139
Disease
Ontology termp-valuen
heart disease2.24e-072


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)
MA0003.10.393314
MA0004.10.0534882
MA0006.10.0136513
MA0007.10.401399
MA0009.10.32421
MA0014.10.145199
MA0017.16.04385
MA0019.10.117831
MA0024.10.247435
MA0025.10.430517
MA0027.11.83568
MA0028.10.37625
MA0029.10.261061
MA0030.10.252948
MA0031.10.208976
MA0038.10.0955329
MA0040.10.265236
MA0041.10.060153
MA0042.10.0489382
MA0043.10.324451
MA0046.10.315924
MA0048.11.16022
MA0050.10.0492315
MA0051.10.643473
MA0052.10.268009
MA0055.11.16517
MA0056.10
MA0057.10.345315
MA0058.10.0259464
MA0059.11.15286
MA0060.10.00245023
MA0061.10.0338355
MA0063.10
MA0066.12.84339
MA0067.10.588512
MA0068.10.00428673
MA0069.10.841084
MA0070.10.30458
MA0071.10.96175
MA0072.10.301215
MA0073.10.0274573
MA0074.10.310475
MA0076.10.29241
MA0077.10.295472
MA0078.10.144889
MA0081.10.0256885
MA0083.10.879076
MA0084.10.758508
MA0087.10.299389
MA0088.10.00803128
MA0089.10
MA0090.10.0334822
MA0091.11.65499
MA0092.11.95068
MA0093.10.014122
MA0095.10
MA0098.10
MA0100.10.683998
MA0101.10.179467
MA0103.11.14492
MA0105.10.955136
MA0106.13.8654
MA0107.10.200883
MA0108.20.206966
MA0109.10
MA0111.10.0372126
MA0113.11.27896
MA0114.12.23473
MA0115.10.52159
MA0116.11.89737
MA0117.10.353309
MA0119.10.452122
MA0122.10.373764
MA0124.10.485991
MA0125.10.415795
MA0130.10
MA0131.10.155349
MA0132.10
MA0133.10
MA0135.10.347651
MA0136.10.0988721
MA0139.10.144669
MA0140.10.0770758
MA0141.12.54037
MA0142.10.188476
MA0143.10.124494
MA0144.10.0243423
MA0145.12.08629
MA0146.10.0265872
MA0147.10.213741
MA0148.10.0625342
MA0149.10.0730455
MA0062.20.158233
MA0035.20.265155
MA0039.20.351538
MA0138.20.145586
MA0002.20.00194829
MA0137.20.0173938
MA0104.20.00241488
MA0047.20.10966
MA0112.21.67445
MA0065.23.91941
MA0150.11.27943
MA0151.10
MA0152.10.0798749
MA0153.10.402047
MA0154.10.724401
MA0155.10.702789
MA0156.10.0178044
MA0157.10.171483
MA0158.10
MA0159.11.18155
MA0160.13.06365
MA0161.10
MA0162.10.00326485
MA0163.12.75125
MA0164.10.131076
MA0080.20.0141356
MA0018.21.22819
MA0099.20.0800285
MA0079.20.00879505
MA0102.20.793085
MA0258.11.98346
MA0259.10.10864
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
TAL1#688653.733577084680030.01042636578680.0386923645811608



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

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