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Coexpression cluster:C1061: Difference between revisions

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{{Coexpression_clusters
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A0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.846854,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.316923,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.028436,MA0056.1;0,MA0057.1;0.305162,MA0058.1;0.950944,MA0059.1;0.948176,MA0060.1;0.190336,MA0061.1;0.961853,MA0063.1;0,MA0066.1;1.3723,MA0067.1;1.23721,MA0068.1;0.415214,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.0136601,MA0074.1;1.36092,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.054222,MA0089.1;0,MA0090.1;0.391903,MA0091.1;2.02209,MA0092.1;0.421159,MA0093.1;0.818737,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;1.49614,MA0103.1;0.792149,MA0105.1;1.47197,MA0106.1;3.62859,MA0107.1;0.666147,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.655057,MA0115.1;1.1606,MA0116.1;1.25157,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.916926,MA0140.1;0.516266,MA0141.1;1.68422,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.623945,MA0145.1;3.58231,MA0146.1;0.418694,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.00915579,MA0138.2;5.16991,MA0002.2;0.531206,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;2.83822,MA0065.2;0.226158,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.974997,MA0155.1;0.0535085,MA0156.1;0.865715,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.682702,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.0163939,MA0163.1;0.493198,MA0164.1;1.51849,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;0.000390427,MA0102.2;1.46209,MA0258.1;1.7796,MA0259.1;0.699589,MA0442.1;0}}
|full_id=C1061_skeletal_Bronchial_pancreas_iPS_diffuse_Mesenchymal_Smooth
|id=C1061
}}

Latest revision as of 11:36, 17 September 2013


Full id: C1061_skeletal_Bronchial_pancreas_iPS_diffuse_Mesenchymal_Smooth



Phase1 CAGE Peaks

Hg19::chr19:3980551..3980576,-p@chr19:3980551..3980576
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Hg19::chr19:3980592..3980608,-p@chr19:3980592..3980608
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Hg19::chr19:3981964..3982023,-p@chr19:3981964..3982023
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Hg19::chr19:3982038..3982062,-p@chr19:3982038..3982062
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Hg19::chr19:3982295..3982322,-p@chr19:3982295..3982322
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Hg19::chr19:3982362..3982381,-p@chr19:3982362..3982381
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Hg19::chr19:3982382..3982401,-p@chr19:3982382..3982401
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Hg19::chr19:3984170..3984233,-p2@EEF2


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>

Cell Type
Ontology termp-valuen
somatic cell2.54e-11588
animal cell1.61e-08679
eukaryotic cell1.61e-08679
electrically responsive cell3.29e-0861
electrically active cell3.29e-0861
contractile cell3.35e-0859
muscle precursor cell1.37e-0758
myoblast1.37e-0758
multi-potent skeletal muscle stem cell1.37e-0758
embryonic cell1.53e-07250
muscle cell1.87e-0755
mesodermal cell2.09e-07121
smooth muscle cell2.71e-0743
smooth muscle myoblast2.71e-0743
Uber Anatomy
Ontology termp-valuen
epithelial vesicle7.29e-1178
somite1.17e-0971
presomitic mesoderm1.17e-0971
presumptive segmental plate1.17e-0971
dermomyotome1.17e-0971
trunk paraxial mesoderm1.17e-0971
dense mesenchyme tissue1.43e-0973
paraxial mesoderm3.38e-0972
presumptive paraxial mesoderm3.38e-0972
multilaminar epithelium1.18e-0883
skeletal muscle tissue6.07e-0862
striated muscle tissue6.07e-0862
myotome6.07e-0862
muscle tissue8.83e-0864
musculature8.83e-0864
musculature of body8.83e-0864
mesoderm3.53e-07315
mesoderm-derived structure3.53e-07315
presumptive mesoderm3.53e-07315
artery4.97e-0742
arterial blood vessel4.97e-0742
arterial system4.97e-0742
trunk mesenchyme8.28e-07122


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)
MA0003.10.393486
MA0004.10.455723
MA0006.10.300178
MA0007.11.95154
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.305162
MA0058.10.950944
MA0059.10.948176
MA0060.10.190336
MA0061.10.961853
MA0063.10
MA0066.11.3723
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0136601
MA0074.11.36092
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.12.02209
MA0092.10.421159
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.11.49614
MA0103.10.792149
MA0105.11.47197
MA0106.13.62859
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.11.25157
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.11.68422
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.13.58231
MA0146.10.418694
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.00915579
MA0138.25.16991
MA0002.20.531206
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.22.83822
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.974997
MA0155.10.0535085
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.493198
MA0164.11.51849
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.000390427
MA0102.21.46209
MA0258.11.7796
MA0259.10.699589
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
CTCF#1066453.350160233171890.007643853146021220.0314892860017873
POLR2A#543082.147453176558070.002210725788971910.0127223931383313



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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