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Coexpression cluster:C1435: Difference between revisions

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0.491474,0.417013,0.000168384,0.21822,0.0137836,0.397562,0.21727,0.351946,0.345508,0.484083,0.144065,0.437432,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.533328,4.62587e-05,0.0476793,0.46896,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.441686,0.369492,0.592234
|tfbs_overrepresentation_for_novel_motifs=1.12961,2.34075,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,1.94918,1.36279,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,2.69471,1.88805,0.436569,1.03374,0.576478,0.387783,1.21515,0.730467,1.10781,1.40695,3.7117,0.547818,0.530785,0.92701,2.26105,0.640661,0.35719,1.30732,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,0.992846,0.468392,0.66382,0.542147,0.0909286,1.02586,0.745008,0.675919,0.455399,1.00488,1.15929,1.57403,0.400834,1.50361,1.04504,0.619193,3.64737,1.59978,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,1.41895,1.15727,5.22491,0.206105,2.39115,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.717596,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.02023,0.32338,0.234532,0.987239,0.776336,2.92493,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.982236,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,4.18682,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.999497,0.524606,1.40818,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,3.23894,0.306342,0.136746,0.308967,1.07915,0.258882,2.69891,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,2.36361
|tfbs_overrepresentation_for_novel_motifs=1.12961,2.34075,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,1.94918,1.36279,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,2.69471,1.88805,0.436569,1.03374,0.576478,0.387783,1.21515,0.730467,1.10781,1.40695,3.7117,0.547818,0.530785,0.92701,2.26105,0.640661,0.35719,1.30732,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,0.992846,0.468392,0.66382,0.542147,0.0909286,1.02586,0.745008,0.675919,0.455399,1.00488,1.15929,1.57403,0.400834,1.50361,1.04504,0.619193,3.64737,1.59978,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,1.41895,1.15727,5.22491,0.206105,2.39115,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.717596,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.02023,0.32338,0.234532,0.987239,0.776336,2.92493,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.982236,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,4.18682,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.999497,0.524606,1.40818,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,3.23894,0.306342,0.136746,0.308967,1.07915,0.258882,2.69891,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,2.36361
|tfbs_overrepresentation_jaspar=MA0003.1;5.21839,MA0004.1;3.45359,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;2.54844,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;0.906394,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;2.74001,MA0058.1;5.23246,MA0059.1;5.22293,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00563817,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;1.61871,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;7.10084,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;1.84113,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;1.16614,MA0146.1;0.441872,MA0147.1;5.32117,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;6.41085,MA0035.2;0.621793,MA0039.2;1.47843,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;1.06611,MA0104.2;2.90014,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;0.132326,MA0155.1;0.65596,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;2.97671,MA0163.1;3.1714,MA0164.1;0.738243,MA0080.2;1.80563,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;3.22572,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: C1435_Renal_lung_retina_Mesenchymal_placenta_Hepatic_uterus



Phase1 CAGE Peaks

Hg19::chr17:40913145..40913205,+p2@RAMP2
Hg19::chr17:40913210..40913221,+p3@RAMP2
Hg19::chr17:40913222..40913233,+p4@RAMP2
Hg19::chr17:40913236..40913252,+p1@RAMP2
Hg19::chr17:40913264..40913273,+p6@RAMP2
Hg19::chr17:72966776..72966789,+p@chr17:72966776..72966789
+


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
adult organism7.87e-34114
anatomical cluster7.17e-22373
anatomical conduit4.89e-19240
tube1.13e-18192
cell layer3.65e-13309
epithelium6.33e-13306
multi-cellular organism5.30e-12656
nervous system1.42e-1189
neurectoderm1.13e-1086
neural tube1.73e-1056
neural rod1.73e-1056
future spinal cord1.73e-1056
neural keel1.73e-1056
central nervous system3.08e-1081
organ system subdivision3.28e-10223
epithelial tube5.28e-10117
blood vessel endothelium9.21e-1018
endothelium9.21e-1018
cardiovascular system endothelium9.21e-1018
regional part of nervous system1.95e-0953
regional part of brain1.95e-0953
neural plate2.19e-0982
presumptive neural plate2.19e-0982
structure with developmental contribution from neural crest1.48e-08132
regional part of forebrain1.71e-0841
forebrain1.71e-0841
anterior neural tube1.71e-0841
future forebrain1.71e-0841
anatomical system2.16e-08624
anatomical group2.90e-08625
brain4.92e-0868
future brain4.92e-0868
embryo7.10e-08592
multi-tissue structure7.42e-08342
compound organ9.94e-0868
splanchnic layer of lateral plate mesoderm9.98e-0883
vessel1.47e-0768
simple squamous epithelium2.24e-0722
squamous epithelium4.43e-0725
germ layer5.23e-07560
germ layer / neural crest5.23e-07560
embryonic tissue5.23e-07560
presumptive structure5.23e-07560
germ layer / neural crest derived structure5.23e-07560
epiblast (generic)5.23e-07560
embryonic structure5.92e-07564
developing anatomical structure5.96e-07581
telencephalon6.43e-0734


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)
MA0003.15.21839
MA0004.13.45359
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.12.54844
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
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.12.74001
MA0058.15.23246
MA0059.15.22293
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.61871
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.17.10084
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
MA0131.11.84113
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
MA0145.11.16614
MA0146.10.441872
MA0147.15.32117
MA0148.10.584698
MA0149.10.612449
MA0062.26.41085
MA0035.20.621793
MA0039.21.47843
MA0138.20.765223
MA0002.20.255126
MA0137.21.06611
MA0104.22.90014
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.12.97671
MA0163.13.1714
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.23.22572
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066443.573504248716680.01316635007238510.0466065765730013
REST#597858.041690596773356.54774545315482e-050.00106186333444416
USF1#739155.30124939767330.0005003327549858890.00441224796064944



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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