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Coexpression cluster:C1492: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.946942,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.635275,0.650887,0.391663,1.06849,0.889639,0.336106,0.236034,0.402028,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,0.225641,0.35719,0.577216,0.35388,0.585658,1.5795,0.248856,0.936389,0.513952,0.0979105,0.390088,0.154075,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.624519,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.181326,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,1.23175,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.986797,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.307168
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.946942,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.635275,0.650887,0.391663,1.06849,0.889639,0.336106,0.236034,0.402028,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,0.225641,0.35719,0.577216,0.35388,0.585658,1.5795,0.248856,0.936389,0.513952,0.0979105,0.390088,0.154075,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.624519,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.181326,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,1.23175,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.986797,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.307168
|tfbs_overrepresentation_jaspar=MA0003.1;0.176622,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.788761,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;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;1.22849,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.0569999,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;1.29635,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.830067,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;0.323925,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;0.811435,MA0145.1;0.347815,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.82735,MA0138.2;0.765223,MA0002.2;0.709311,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.354331,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.819655,MA0155.1;0.65596,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.875329,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.347838,MA0163.1;0.273773,MA0164.1;0.738243,MA0080.2;1.02158,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.166826,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:58, 22 January 2013


Full id: C1492_chorionic_amniotic_Smooth_basal_spindle_placenta_mesenchymal



Phase1 CAGE Peaks

Hg19::chr22:33197683..33197698,+p1@TIMP3
Hg19::chr22:33253227..33253256,+p@chr22:33253227..33253256
+
Hg19::chr22:33255260..33255310,-p2@CU676956
Hg19::chr22:33255345..33255482,-p1@CU676956
Hg19::chr22:33256226..33256238,-p4@ENST00000327661
Hg19::chr22:33256911..33256925,+p3@TIMP3


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:0008191metalloendopeptidase inhibitor activity0.00900741787354292
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0227077761517889
GO:0050953sensory perception of light stimulus0.0227077761517889
GO:0007601visual perception0.0227077761517889
GO:0004866endopeptidase inhibitor activity0.0227077761517889
GO:0030414protease inhibitor activity0.0227077761517889
GO:0007167enzyme linked receptor protein signaling pathway0.0227077761517889
GO:0004857enzyme inhibitor activity0.0247851171553044
GO:0005578proteinaceous extracellular matrix0.0247851171553044
GO:0044421extracellular region part0.0457596095179988
GO:0007600sensory perception0.0457596095179988



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
fibroblast1.10e-1176
preadipocyte5.67e-0812
smooth muscle cell5.96e-0743
smooth muscle myoblast5.96e-0743
muscle cell6.08e-0755
Uber Anatomy
Ontology termp-valuen
organ component layer5.13e-1266
multi-tissue structure1.96e-10342
multi-cellular organism4.18e-10656
adult organism9.50e-10114
surface structure7.03e-0999
dense mesenchyme tissue2.07e-0873
anatomical system3.23e-08624
structure with developmental contribution from neural crest3.47e-08132
organ part4.23e-08218
anatomical group5.06e-08625
paraxial mesoderm5.35e-0872
presumptive paraxial mesoderm5.35e-0872
somite5.73e-0871
presomitic mesoderm5.73e-0871
presumptive segmental plate5.73e-0871
dermomyotome5.73e-0871
trunk paraxial mesoderm5.73e-0871
epithelial vesicle8.05e-0878
trunk mesenchyme9.94e-08122
extraembryonic membrane1.33e-0714
membranous layer1.33e-0714
muscle tissue1.67e-0764
musculature1.67e-0764
musculature of body1.67e-0764
anatomical cluster1.85e-07373
cell layer3.09e-07309
organism subdivision3.18e-07264
skeletal muscle tissue3.58e-0762
striated muscle tissue3.58e-0762
myotome3.58e-0762
multilaminar epithelium3.61e-0783
integument4.44e-0746
integumental system4.44e-0746
epithelium7.17e-07306
adipose tissue7.46e-0714


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
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.788761
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
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.22849
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0569999
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.11.29635
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
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
MA0144.10.811435
MA0145.10.347815
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.82735
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.10.273773
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.20.166826
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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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