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Coexpression cluster:C510: Difference between revisions

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{{Coexpression_clusters
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834,0.719642,0.590036,0.86438,0.249584,0.660181,0.0686399,0.445395,0.907598,0.784583,0.752806,0.453778,0.41671,0.665994,0.311997,0.278177,0.565897,0.357633,0.294452,0.472167,0.0669542,0.686837,0.641805,0.427959,0.255632,0.402522,0.749736|tfbs_overrepresentation_for_novel_motifs=0.81962,0.0582092,0.127744,0.226461,0.336835,1.19634,0.283394,1.51281,0.169427,0.0402811,0.203249,1.53852,0.288598,0.753523,0.334774,0.370545,0.469711,0.546349,0.315616,0.408826,2.54503,0.126722,0.626287,1.64578,0.156949,0.336616,0.748412,0.217946,0.104779,0.998436,0.187767,0.502277,0.0585266,0.0299027,0.0841935,0.0511197,0.0825354,0.64174,0.0708005,0.148458,0.594507,0.176475,0.066746,0.332492,0.130655,0.147132,0.284252,0.195517,0.0578392,0.341709,0.348337,0.293583,0.145063,0.571408,0.712611,0.276665,0.707757,0.700573,0.411389,0.698795,0.538962,0.286121,0.385159,1.97893,0.300385,0.415664,0.795966,1.15172,0.493047,0.993712,0.167519,1.09738,0.0516651,0.710737,0.0277888,0.024084,0.226496,0.430778,0.490165,0.152902,0.930949,1.13034,0.300103,0.396445,0.662744,0.0156241,0.0376191,0.0803602,0.370044,1.24919,0.885103,0.637733,0.517273,0.833906,0.103441,0.239995,0.570556,0.555608,0.373917,0.0668763,0.25011,0.512221,0.550563,0.472938,0.405789,0.200011,0.45903,0.27168,0.156782,0.0941477,0.419252,0.548062,0.124365,0.210038,0.839147,0.0817205,0.00083804,0.186928,1.06343,0.844523,0.702982,0.368007,0.22321,0.309149,0.945405,0.431436,0.762734,0.521744,0.742996,0.241301,0.638371,1.05797,0.756554,0.30647,0.897471,0.0161899,0.183595,0.62352,0.856781,1.69932,1.30076,0.82115,0.765828,0.552418,0.407293,0.685667,0.393075,1.5412,0.174198,0.47494,0.0443587,0.00309082,0.638724,0.365733,0.285738,1.0234,0.356515,0.651485,0.475228,0.13835,0.819992,0.621644,0.489467,0.433659,0.421111,0.299472,0.445457,0.282346,0.00228002|tfbs_overrepresentation_jaspar=MA0003.1;0.00101787,MA0004.1;1.76461,MA0006.1;0.101986,MA0007.1;0.564363,MA0009.1;0.600198,MA0014.1;0.0124091,MA0017.1;0.125342,MA0019.1;0.322194,MA0024.1;0.50459,MA0025.1;0.725013,MA0027.1;2.18072,MA0028.1;0.358818,MA0029.1;1.29635,MA0030.1;0.511665,MA0031.1;0.454061,MA0038.1;0.285594,MA0040.1;0.527306,MA0041.1;0.628965,MA0042.1;0.197306,MA0043.1;0.60049,MA0046.1;0.590147,MA0048.1;0.151328,MA0050.1;0.574987,MA0051.1;0.282227,MA0052.1;1.31505,MA0055.1;0.0623184,MA0056.1;0,MA0057.1;0.0104156,MA0058.1;1.997,MA0059.1;1.9903,MA0060.1;0.384884,MA0061.1;1.78123,MA0063.1;0,MA0066.1;0.285934,MA0067.1;0.900956,MA0068.1;0.0222576,MA0069.1;0.586593,MA0070.1;0.576293,MA0071.1;0.255111,MA0072.1;0.572162,MA0073.1;4.73229e-07,MA0074.1;0.770086,MA0076.1;0.902204,MA0077.1;0.565087,MA0078.1;0.363755,MA0081.1;0.434032,MA0083.1;0.607144,MA0084.1;1.08294,MA0087.1;1.39781,MA0088.1;0.673545,MA0089.1;0,MA0090.1;0.485893,MA0091.1;0.601165,MA0092.1;0.53622,MA0093.1;2.28499,MA0095.1;0,MA0098.1;0,MA0100.1;0.296726,MA0101.1;1.15589,MA0103.1;0.0967439,MA0105.1;0.970472,MA0106.1;0.319,MA0107.1;2.3995,MA0108.2;0.451357,MA0109.1;0,MA0111.1;0.170509,MA0113.1;0.884817,MA0114.1;0.228885,MA0115.1;0.827474,MA0116.1;0.0681676,MA0117.1;0.635078,MA0119.1;0.407815,MA0122.1;0.659244,MA0124.1;0.787807,MA0125.1;0.708116,MA0130.1;0,MA0131.1;0.379172,MA0132.1;0,MA0133.1;0,MA0135.1;0.628343,MA0136.1;0.291242,MA0139.1;0.0300305,MA0140.1;0.253051,MA0141.1;0.430939,MA0142.1;0.426146,MA0143.1;0.885144,MA0144.1;0.209582,MA0145.1;0.00456382,MA0146.1;0.00247058,MA0147.1;1.35064,MA0148.1;0.225411,MA0149.1;0.245595,MA0062.2;0.309868,MA0035.2;0.252505,MA0039.2;9.54563e-05,MA0138.2;0.364793,MA0002.2;0.357374,MA0137.2;0.368913,MA0104.2;1.05445,MA0047.2;0.309071,MA0112.2;0.0229828,MA0065.2;0.0273646,MA0150.1;0.476082,MA0151.1;0,MA0152.1;0.258148,MA0153.1;0.692238,MA0154.1;0.0413356,MA0155.1;0.0203861,MA0156.1;0.372479,MA0157.1;0.402372,MA0158.1;0,MA0159.1;0.527394,MA0160.1;0.236884,MA0161.1;0,MA0162.1;0.000261548,MA0163.1;0.000900095,MA0164.1;0.342871,MA0080.2;0.338854,MA0018.2;0.320136,MA0099.2;0.716923,MA0079.2;7.63574e-12,MA0102.2;1.11935,MA0258.1;0.053266,MA0259.1;0.547239,MA0442.1;0}}
|full_id=C510_fibrous_mesothelioma_cholangiocellular_liposarcoma_Fibroblast_mesenchymal_leukemia
|id=C510
}}

Latest revision as of 11:24, 17 September 2013


Full id: C510_fibrous_mesothelioma_cholangiocellular_liposarcoma_Fibroblast_mesenchymal_leukemia



Phase1 CAGE Peaks

Hg19::chr11:101742272..101742276,-p@chr11:101742272..101742276
-
Hg19::chr11:81549961..81549965,-p@chr11:81549961..81549965
-
Hg19::chr11:81551043..81551054,-p@chr11:81551043..81551054
-
Hg19::chr12:127737083..127737103,-p@chr12:127737083..127737103
-
Hg19::chr16:77317713..77317723,+p1@CU687665
Hg19::chr18:71197490..71197495,-p@chr18:71197490..71197495
-
Hg19::chr3:55178388..55178399,-p@chr3:55178388..55178399
-
Hg19::chr4:177796841..177796851,+p1@ENST00000508790
Hg19::chr5:14034644..14034647,-p@chr5:14034644..14034647
-
Hg19::chr5:27742047..27742052,-p@chr5:27742047..27742052
-
Hg19::chr6:68596984..68596998,-p@chr6:68596984..68596998
-
Hg19::chr6:68597008..68597030,-p@chr6:68597008..68597030
-
Hg19::chr7:119353807..119353812,-p@chr7:119353807..119353812
-
Hg19::chr8:119905427..119905438,-p@chr8:119905427..119905438
-
Hg19::chr8:119905454..119905469,-p@chr8:119905454..119905469
-
Hg19::chr8:119919156..119919163,+p@chr8:119919156..119919163
+
Hg19::chr8:23564065..23564087,-p1@NKX2-6
Hg19::chr9:118412488..118412525,-p@chr9:118412488..118412525
-


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:0035050embryonic heart tube development0.00844813375721182
GO:0007507heart development0.0470681737901801
GO:0035295tube development0.0470681737901801



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>disease_data<br>

Cell Type
Ontology termp-valuen
bone matrix secreting cell1.55e-982
osteocyte1.55e-982
osteoclast1.55e-982
bone marrow cell3.81e-2110
osteoblast2.25e-1911
osteoprogenitor cell2.25e-1911
mesenchyme condensation cell2.25e-1911
single fate stem cell2.29e-1120
secretory cell5.81e-0736
Uber Anatomy
Ontology termp-valuen
zone of skin3.10e-504


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)
MA0003.10.00101787
MA0004.11.76461
MA0006.10.101986
MA0007.10.564363
MA0009.10.600198
MA0014.10.0124091
MA0017.10.125342
MA0019.10.322194
MA0024.10.50459
MA0025.10.725013
MA0027.12.18072
MA0028.10.358818
MA0029.11.29635
MA0030.10.511665
MA0031.10.454061
MA0038.10.285594
MA0040.10.527306
MA0041.10.628965
MA0042.10.197306
MA0043.10.60049
MA0046.10.590147
MA0048.10.151328
MA0050.10.574987
MA0051.10.282227
MA0052.11.31505
MA0055.10.0623184
MA0056.10
MA0057.10.0104156
MA0058.11.997
MA0059.11.9903
MA0060.10.384884
MA0061.11.78123
MA0063.10
MA0066.10.285934
MA0067.10.900956
MA0068.10.0222576
MA0069.10.586593
MA0070.10.576293
MA0071.10.255111
MA0072.10.572162
MA0073.14.73229e-07
MA0074.10.770086
MA0076.10.902204
MA0077.10.565087
MA0078.10.363755
MA0081.10.434032
MA0083.10.607144
MA0084.11.08294
MA0087.11.39781
MA0088.10.673545
MA0089.10
MA0090.10.485893
MA0091.10.601165
MA0092.10.53622
MA0093.12.28499
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.11.15589
MA0103.10.0967439
MA0105.10.970472
MA0106.10.319
MA0107.12.3995
MA0108.20.451357
MA0109.10
MA0111.10.170509
MA0113.10.884817
MA0114.10.228885
MA0115.10.827474
MA0116.10.0681676
MA0117.10.635078
MA0119.10.407815
MA0122.10.659244
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.291242
MA0139.10.0300305
MA0140.10.253051
MA0141.10.430939
MA0142.10.426146
MA0143.10.885144
MA0144.10.209582
MA0145.10.00456382
MA0146.10.00247058
MA0147.11.35064
MA0148.10.225411
MA0149.10.245595
MA0062.20.309868
MA0035.20.252505
MA0039.29.54563e-05
MA0138.20.364793
MA0002.20.357374
MA0137.20.368913
MA0104.21.05445
MA0047.20.309071
MA0112.20.0229828
MA0065.20.0273646
MA0150.10.476082
MA0151.10
MA0152.10.258148
MA0153.10.692238
MA0154.10.0413356
MA0155.10.0203861
MA0156.10.372479
MA0157.10.402372
MA0158.10
MA0159.10.527394
MA0160.10.236884
MA0161.10
MA0162.10.000261548
MA0163.10.000900095
MA0164.10.342871
MA0080.20.338854
MA0018.20.320136
MA0099.20.716923
MA0079.27.63574e-12
MA0102.21.11935
MA0258.10.053266
MA0259.10.547239
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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