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Coexpression cluster:C1434: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.946942,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,1.18908,1.56773,0.391663,0.415981,0.889639,0.892779,0.236034,0.402028,2.9028,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,1.40695,0.396295,1.04549,0.530785,0.92701,0.816912,0.225641,2.52957,4.05712,0.35388,0.585658,0.329602,1.28576,0.355745,0.513952,0.0979105,1.01199,0.0393783,0.468392,0.66382,0.542147,0.0909286,1.02586,0.745008,0.675919,0.149032,1.00488,1.15929,1.57403,0.400834,0.62023,2.34444,1.50144,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,3.20696,0.500342,0.275507,0.146905,1.15727,0.218784,0.594475,3.17015,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,2.50005,0.0481066,0.398737,1.62415,0.771626,1.71797,1.34233,3.98428,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,2.92493,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,1.56033,0.483695,1.74379,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.460936,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,2.18236,1.1919,0.324369,1.07876,0.53374,1.20639,1.65434,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,1.27188,0.306342,0.424432,0.639143,1.07915,0.258882,1.59875,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_for_novel_motifs=1.12961,0.946942,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,1.18908,1.56773,0.391663,0.415981,0.889639,0.892779,0.236034,0.402028,2.9028,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,1.40695,0.396295,1.04549,0.530785,0.92701,0.816912,0.225641,2.52957,4.05712,0.35388,0.585658,0.329602,1.28576,0.355745,0.513952,0.0979105,1.01199,0.0393783,0.468392,0.66382,0.542147,0.0909286,1.02586,0.745008,0.675919,0.149032,1.00488,1.15929,1.57403,0.400834,0.62023,2.34444,1.50144,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,3.20696,0.500342,0.275507,0.146905,1.15727,0.218784,0.594475,3.17015,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,2.50005,0.0481066,0.398737,1.62415,0.771626,1.71797,1.34233,3.98428,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,2.92493,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,1.56033,0.483695,1.74379,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.460936,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,2.18236,1.1919,0.324369,1.07876,0.53374,1.20639,1.65434,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,1.27188,0.306342,0.424432,0.639143,1.07915,0.258882,1.59875,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_jaspar=MA0003.1;0.176622,MA0004.1;0.558729,MA0006.1;1.79433,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.108006,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;2.08744,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.213007,MA0056.1;0,MA0057.1;0.450439,MA0058.1;1.16137,MA0059.1;1.15845,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;2.43863,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.51617,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;1.22966,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;1.02138,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;1.55935,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.347815,MA0146.1;0.232472,MA0147.1;1.57246,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.0313803,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;2.08061,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;1.3291,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.347838,MA0163.1;0.273773,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.0607789,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;1.6038,MA0442.1;0
}}
}}

Revision as of 19:56, 22 January 2013


Full id: C1434_Olfactory_leiomyoma_Adipocyte_Hair_tenocyte_Preadipocyte_Smooth



Phase1 CAGE Peaks

Hg19::chr17:40556364..40556401,-p@chr17:40556364..40556401
-
Hg19::chr17:40556677..40556728,-p@chr17:40556677..40556728
-
Hg19::chr17:40557069..40557101,-p8@PTRF
Hg19::chr17:40557111..40557154,-p5@PTRF
Hg19::chr17:40557183..40557202,-p10@PTRF
Hg19::chr17:40557206..40557266,-p6@PTRF


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
splanchnic layer of lateral plate mesoderm3.11e-2183
vasculature4.88e-2178
vascular system4.88e-2178
epithelial vesicle1.05e-2078
vessel6.74e-2068
epithelial tube open at both ends2.20e-1959
blood vessel2.20e-1959
blood vasculature2.20e-1959
vascular cord2.20e-1959
unilaminar epithelium6.16e-19148
trunk mesenchyme2.32e-18122
multilaminar epithelium2.33e-1883
somite4.45e-1871
presomitic mesoderm4.45e-1871
presumptive segmental plate4.45e-1871
dermomyotome4.45e-1871
trunk paraxial mesoderm4.45e-1871
dense mesenchyme tissue5.00e-1873
mesenchyme7.87e-18160
entire embryonic mesenchyme7.87e-18160
paraxial mesoderm9.18e-1872
presumptive paraxial mesoderm9.18e-1872
epithelial tube1.36e-17117
artery2.32e-1642
arterial blood vessel2.32e-1642
arterial system2.32e-1642
organism subdivision4.18e-16264
muscle tissue1.49e-1564
musculature1.49e-1564
musculature of body1.49e-1564
skeletal muscle tissue2.51e-1562
striated muscle tissue2.51e-1562
myotome2.51e-1562
circulatory system4.45e-14112
cardiovascular system5.31e-14109
trunk5.85e-14199
cell layer8.29e-14309
epithelium1.35e-13306
surface structure2.11e-1399
multi-cellular organism8.79e-13656
systemic artery2.25e-1233
systemic arterial system2.25e-1233
multi-tissue structure4.09e-12342
anatomical system1.10e-10624
anatomical group1.47e-10625
anatomical cluster4.81e-10373
integument1.63e-0946
integumental system1.63e-0946
anatomical conduit2.48e-09240
mesoderm3.45e-09315
mesoderm-derived structure3.45e-09315
presumptive mesoderm3.45e-09315
skin of body8.78e-0841
organ component layer2.33e-0766
aorta3.51e-0721
aortic system3.51e-0721
squamous epithelium5.42e-0725
compound organ8.88e-0768


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)
MA0003.10.176622
MA0004.10.558729
MA0006.11.79433
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.12.08744
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.450439
MA0058.11.16137
MA0059.11.15845
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.12.43863
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.51617
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.11.55935
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.232472
MA0147.11.57246
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0313803
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.22.08061
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.3291
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.0607789
MA0102.21.58513
MA0258.10.289793
MA0259.11.6038
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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