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Coexpression cluster:C764: Difference between revisions

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{{Coexpression_clusters
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|full_id=C764_Olfactory_Mesenchymal_Synoviocyte_Adipocyte_tenocyte_Chondrocyte_Multipotent
|id=C764
}}

Latest revision as of 11:30, 17 September 2013


Full id: C764_Olfactory_Mesenchymal_Synoviocyte_Adipocyte_tenocyte_Chondrocyte_Multipotent



Phase1 CAGE Peaks

Hg19::chr19:48244361..48244372,+p3@EHD2
Hg19::chr19:48244802..48244816,+p2@EHD2
Hg19::chr19:48244862..48244878,+p3@AK301380
Hg19::chr19:48244887..48244893,+p7@AK301380
Hg19::chr19:48244924..48244976,-p2@CU677000
Hg19::chr19:48245099..48245147,-p1@CU677000
Hg19::chr19:48245226..48245235,+p5@AK301380
Hg19::chr19:48245284..48245309,+p1@AK301380
Hg19::chr19:48245317..48245328,+p6@AK301380
Hg19::chr19:48245342..48245364,+p2@AK301380
Hg19::chr19:48245424..48245454,+p4@AK301380


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:0030866cortical actin cytoskeleton organization and biogenesis0.0100965501000824
GO:0030865cortical cytoskeleton organization and biogenesis0.0100965501000824
GO:0019904protein domain specific binding0.0455146068003715
GO:0010324membrane invagination0.0455146068003715
GO:0006897endocytosis0.0455146068003715
GO:0030036actin cytoskeleton organization and biogenesis0.0455146068003715
GO:0030029actin filament-based process0.0455146068003715
GO:0003924GTPase activity0.0455146068003715
GO:0016044membrane organization and biogenesis0.0455146068003715



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
epithelial vesicle1.62e-1978
multilaminar epithelium1.06e-1783
somite7.13e-1771
presomitic mesoderm7.13e-1771
presumptive segmental plate7.13e-1771
dermomyotome7.13e-1771
trunk paraxial mesoderm7.13e-1771
dense mesenchyme tissue8.95e-1773
paraxial mesoderm1.97e-1672
presumptive paraxial mesoderm1.97e-1672
mesenchyme2.76e-16160
entire embryonic mesenchyme2.76e-16160
splanchnic layer of lateral plate mesoderm1.17e-1583
trunk mesenchyme1.32e-15122
vasculature2.54e-1578
vascular system2.54e-1578
muscle tissue3.43e-1564
musculature3.43e-1564
musculature of body3.43e-1564
skeletal muscle tissue3.71e-1562
striated muscle tissue3.71e-1562
myotome3.71e-1562
organism subdivision1.71e-14264
surface structure1.91e-1499
unilaminar epithelium5.96e-14148
cell layer2.98e-13309
vessel3.52e-1368
epithelium5.26e-13306
epithelial tube8.98e-13117
epithelial tube open at both ends1.17e-1259
blood vessel1.17e-1259
blood vasculature1.17e-1259
vascular cord1.17e-1259
trunk1.81e-12199
multi-tissue structure7.05e-12342
multi-cellular organism5.25e-11656
artery9.62e-1142
arterial blood vessel9.62e-1142
arterial system9.62e-1142
cardiovascular system3.80e-10109
circulatory system4.81e-10112
integument5.15e-1046
integumental system5.15e-1046
anatomical system2.58e-09624
anatomical cluster2.97e-09373
anatomical group4.32e-09625
systemic artery1.95e-0833
systemic arterial system1.95e-0833
skin of body4.67e-0841
anatomical conduit9.45e-08240


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)
MA0003.10.138892
MA0004.10.349539
MA0006.12.51915
MA0007.10.332734
MA0009.13.09387
MA0014.10.79286
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.480412
MA0056.10
MA0057.10.176435
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.13.62623
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.943943
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.0490843
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.467716
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.12.55605
MA0103.10.203171
MA0105.13.03609
MA0106.10.482519
MA0107.12.83653
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.12.15438
MA0114.10.153042
MA0115.11.02805
MA0116.12.86229
MA0117.10.827487
MA0119.13.66227
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.11.14308
MA0139.12.15238
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.12.69183
MA0145.10.515404
MA0146.10.00165539
MA0147.10.488526
MA0148.10.372124
MA0149.136.0779
MA0062.20.320507
MA0035.22.75508
MA0039.21.48374
MA0138.20.534556
MA0002.22.36838
MA0137.21.21272
MA0104.20.118985
MA0047.20.47109
MA0112.22.02459
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.353037
MA0155.10.74825
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.11.0031
MA0161.10
MA0162.10.00470038
MA0163.19.54139
MA0164.10.509774
MA0080.20.611699
MA0018.20.483823
MA0099.20.411824
MA0079.21.17095
MA0102.21.32663
MA0258.12.61991
MA0259.10.504687
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

No analysis results for this cluster

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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