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Coexpression cluster:C339: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0362237,5.95245,0.584729,2.09568,0.470143,1.52028,0.785405,0.00553043,0.346227,0.000153094,0.544811,0.889944,0.120833,1.8072,0.0233485,2.67268,1.34778,0.0132576,0.430654,0.0533521,1.77984,10.8285,0.0832693,0.0225281,0.407145,0.162121,0.31208,2.03201,0.0243516,0.00787101,0.0647008,0.292383,0.125715,1.43952,0.196304,1.13649,0.016104,1.02829,2.41351,0.479051,0.0164232,0.806698,0.0235147,0.0230134,0.283653,0.378189,0.394651,2.44217,0.00189707,0.0243809,2.96717,2.58358,0.0822334,3.43685,0.475837,0.765144,0.0253589,0.103222,0.0285692,0.102726,0.32323,0.126376,0.00535723,0.245859,0.136236,0.222166,0.551996,0.889382,0.284717,0.737624,0.0536708,0.207931,0.149595,0.474142,0.00227848,0.970894,0.637659,0.234122,0.282332,0.0461435,1.95848,1.96896,0.136039,0.00577942,0.431067,0.395006,0.0518048,0.391304,0.186966,0.984017,0.634935,0.408872,0.304922,0.00966404,0.0238196,0.0114314,0.258701,0.337414,0.1899,0.486729,0.0125039,0.300686,0.333104,1.35752,0.214431,0.535136,0.256823,0.750137,0.406652,1.8557,0.341703,0.330971,0.0326221,3.23432,0.592003,6.31411,0.675922,1.7958,1.17847,3.79591,0.467142,3.93258,0.0855095,0.14239,0.691757,0.234645,0.121127,0.30868,0.503421,3.39068,0.409436,1.81777,0.515797,0.140501,0.646547,0.000840633,0.062374,4.04359,0.608436,1.42699,1.03434,0.575287,0.122045,0.334687,7.20563,0.099088,0.204563,1.27059,14.8668,0.0092535,0.669201,4.35735,0.409747,1.37681,0.126114,0.765951,1.5952,0.0206573,0.0482085,2.99852,0.574213,0.394694,0.281754,1.90874,0.226459,0.833847,5.91151,0.123801,0.713585
|tfbs_overrepresentation_for_novel_motifs=0.0362237,5.95245,0.584729,2.09568,0.470143,1.52028,0.785405,0.00553043,0.346227,0.000153094,0.544811,0.889944,0.120833,1.8072,0.0233485,2.67268,1.34778,0.0132576,0.430654,0.0533521,1.77984,10.8285,0.0832693,0.0225281,0.407145,0.162121,0.31208,2.03201,0.0243516,0.00787101,0.0647008,0.292383,0.125715,1.43952,0.196304,1.13649,0.016104,1.02829,2.41351,0.479051,0.0164232,0.806698,0.0235147,0.0230134,0.283653,0.378189,0.394651,2.44217,0.00189707,0.0243809,2.96717,2.58358,0.0822334,3.43685,0.475837,0.765144,0.0253589,0.103222,0.0285692,0.102726,0.32323,0.126376,0.00535723,0.245859,0.136236,0.222166,0.551996,0.889382,0.284717,0.737624,0.0536708,0.207931,0.149595,0.474142,0.00227848,0.970894,0.637659,0.234122,0.282332,0.0461435,1.95848,1.96896,0.136039,0.00577942,0.431067,0.395006,0.0518048,0.391304,0.186966,0.984017,0.634935,0.408872,0.304922,0.00966404,0.0238196,0.0114314,0.258701,0.337414,0.1899,0.486729,0.0125039,0.300686,0.333104,1.35752,0.214431,0.535136,0.256823,0.750137,0.406652,1.8557,0.341703,0.330971,0.0326221,3.23432,0.592003,6.31411,0.675922,1.7958,1.17847,3.79591,0.467142,3.93258,0.0855095,0.14239,0.691757,0.234645,0.121127,0.30868,0.503421,3.39068,0.409436,1.81777,0.515797,0.140501,0.646547,0.000840633,0.062374,4.04359,0.608436,1.42699,1.03434,0.575287,0.122045,0.334687,7.20563,0.099088,0.204563,1.27059,14.8668,0.0092535,0.669201,4.35735,0.409747,1.37681,0.126114,0.765951,1.5952,0.0206573,0.0482085,2.99852,0.574213,0.394694,0.281754,1.90874,0.226459,0.833847,5.91151,0.123801,0.713585
|tfbs_overrepresentation_jaspar=MA0003.1;0.0199506,MA0004.1;1.41161,MA0006.1;0.246818,MA0007.1;0.0679494,MA0009.1;0.375925,MA0014.1;0.440157,MA0017.1;0.0330569,MA0019.1;0.151679,MA0024.1;0.294311,MA0025.1;0.487069,MA0027.1;1.90579,MA0028.1;0.027018,MA0029.1;0.308904,MA0030.1;0.300221,MA0031.1;0.703934,MA0038.1;0.126016,MA0040.1;0.313366,MA0041.1;0.0839596,MA0042.1;0.070122,MA0043.1;0.376179,MA0046.1;0.367181,MA0048.1;0.000441415,MA0050.1;0.0704881,MA0051.1;0.12372,MA0052.1;0.316327,MA0055.1;0.00401726,MA0056.1;0,MA0057.1;1.53968,MA0058.1;1.00687,MA0059.1;1.00159,MA0060.1;0.00534716,MA0061.1;0.0199515,MA0063.1;0,MA0066.1;0.126249,MA0067.1;1.56551,MA0068.1;0.921806,MA0069.1;0.364099,MA0070.1;0.355189,MA0071.1;2.30675,MA0072.1;1.65709,MA0073.1;32.4812,MA0074.1;0.123313,MA0076.1;1.07237,MA0077.1;0.345539,MA0078.1;0.182227,MA0081.1;0.0400838,MA0083.1;0.381987,MA0084.1;0.823032,MA0087.1;0.349692,MA0088.1;0.370125,MA0089.1;0,MA0090.1;0.0504181,MA0091.1;0.561757,MA0092.1;5.80795,MA0093.1;1.98377,MA0095.1;0,MA0098.1;0,MA0100.1;4.12815,MA0101.1;0.0246931,MA0103.1;0.0212236,MA0105.1;0.0089638,MA0106.1;0.14939,MA0107.1;0.011011,MA0108.2;0.69888,MA0109.1;0,MA0111.1;0.055257,MA0113.1;2.13815,MA0114.1;0.286723,MA0115.1;0.581155,MA0116.1;0.0115061,MA0117.1;1.04791,MA0119.1;1.34171,MA0122.1;1.91981,MA0124.1;0.544476,MA0125.1;0.471774,MA0130.1;0,MA0131.1;2.39821,MA0132.1;0,MA0133.1;0,MA0135.1;0.400588,MA0136.1;2.56692,MA0139.1;0.837938,MA0140.1;0.104326,MA0141.1;0.355203,MA0142.1;0.230443,MA0143.1;0.159255,MA0144.1;0.122937,MA0145.1;1.51878,MA0146.1;5.7165,MA0147.1;0.314268,MA0148.1;0.0868592,MA0149.1;0.0995233,MA0062.2;0.00301306,MA0035.2;0.103973,MA0039.2;2.58349,MA0138.2;0.183007,MA0002.2;0.503296,MA0137.2;0.0286334,MA0104.2;0.0879339,MA0047.2;0.142334,MA0112.2;1.6991,MA0065.2;2.52186,MA0150.1;0.0483839,MA0151.1;0,MA0152.1;0.107647,MA0153.1;0.457467,MA0154.1;0.00191347,MA0155.1;3.26224,MA0156.1;0.120803,MA0157.1;0.211768,MA0158.1;0,MA0159.1;0.0121148,MA0160.1;0.0939956,MA0161.1;0,MA0162.1;0.130474,MA0163.1;0.371453,MA0164.1;0.166704,MA0080.2;1.52474,MA0018.2;0.896155,MA0099.2;0.107829,MA0079.2;16.4201,MA0102.2;0.858102,MA0258.1;0.0390558,MA0259.1;0.561281,MA0442.1;0
}}
}}

Revision as of 19:05, 22 January 2013


Full id: C339_Mesenchymal_heart_leiomyoma_Adipocyte_Smooth_skeletal_tongue



Phase1 CAGE Peaks

Hg19::chr19:36245601..36245615,-p3@CU679244
Hg19::chr19:36245605..36245616,+p@chr19:36245605..36245616
+
Hg19::chr19:36245653..36245670,-p4@CU679244
Hg19::chr19:36245680..36245700,+p@chr19:36245680..36245700
+
Hg19::chr19:36245682..36245706,-p1@CU679244
Hg19::chr19:36245714..36245739,+p@chr19:36245714..36245739
+
Hg19::chr19:36245719..36245738,-p2@CU679244
Hg19::chr19:36245740..36245750,+p@chr19:36245740..36245750
+
Hg19::chr19:36245757..36245768,+p@chr19:36245757..36245768
+
Hg19::chr19:36245789..36245798,-p20@HSPB6
Hg19::chr19:36245828..36245846,-p4@HSPB6
Hg19::chr19:36245853..36245881,-p5@HSPB6
Hg19::chr19:36245884..36245902,-p8@HSPB6
Hg19::chr19:36245935..36245985,-p3@HSPB6
Hg19::chr19:36245962..36245977,+p@chr19:36245962..36245977
+
Hg19::chr19:36245984..36246010,+p@chr19:36245984..36246010
+
Hg19::chr19:36245988..36246002,-p15@HSPB6
Hg19::chr19:36246007..36246015,-p19@HSPB6
Hg19::chr19:36246020..36246050,+p@chr19:36246020..36246050
+
Hg19::chr19:36246042..36246059,-p9@HSPB6
Hg19::chr19:36246080..36246107,+p@chr19:36246080..36246107
+
Hg19::chr19:36246086..36246335,-p2@HSPB6
Hg19::chr19:36246113..36246265,+p@chr19:36246113..36246265
+
Hg19::chr19:36246354..36246383,-p6@HSPB6
Hg19::chr19:36246384..36246401,-p7@HSPB6
Hg19::chr19:36246404..36246415,-p14@HSPB6
Hg19::chr19:36246439..36246461,+p@chr19:36246439..36246461
+
Hg19::chr19:36246480..36246491,-p13@HSPB6
Hg19::chr19:36246494..36246501,-p21@HSPB6
Hg19::chr19:36246502..36246515,-p11@HSPB6
Hg19::chr19:36246564..36246573,-p24@HSPB6
Hg19::chr19:36246722..36246741,-p16@HSPB6
Hg19::chr19:36246747..36246780,-p10@HSPB6
Hg19::chr19:36247921..36247937,-p1@HSPB6


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
muscle tissue6.80e-2264
musculature6.80e-2264
musculature of body6.80e-2264
skeletal muscle tissue7.84e-2162
striated muscle tissue7.84e-2162
myotome7.84e-2162
dense mesenchyme tissue1.69e-1973
paraxial mesoderm3.14e-1972
presumptive paraxial mesoderm3.14e-1972
somite4.46e-1971
presomitic mesoderm4.46e-1971
presumptive segmental plate4.46e-1971
dermomyotome4.46e-1971
trunk paraxial mesoderm4.46e-1971
epithelial vesicle1.57e-1578
multilaminar epithelium2.35e-1583
mesenchyme9.86e-14160
entire embryonic mesenchyme9.86e-14160
trunk mesenchyme1.97e-13122
tissue5.98e-12773
adult organism1.33e-11114
primary circulatory organ2.41e-1027
adipose tissue3.79e-1014
multi-tissue structure4.65e-09342
mesoderm4.99e-09315
mesoderm-derived structure4.99e-09315
presumptive mesoderm4.99e-09315
splanchnic layer of lateral plate mesoderm6.54e-0983
smooth muscle tissue2.06e-0815
heart2.89e-0824
primitive heart tube2.89e-0824
primary heart field2.89e-0824
anterior lateral plate mesoderm2.89e-0824
heart tube2.89e-0824
heart primordium2.89e-0824
cardiac mesoderm2.89e-0824
cardiogenic plate2.89e-0824
heart rudiment2.89e-0824
trunk9.08e-08199
multi-cellular organism1.35e-07656
cell layer2.66e-07309
epithelium3.34e-07306
systemic artery8.56e-0733
systemic arterial system8.56e-0733


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)
MA0003.10.0199506
MA0004.11.41161
MA0006.10.246818
MA0007.10.0679494
MA0009.10.375925
MA0014.10.440157
MA0017.10.0330569
MA0019.10.151679
MA0024.10.294311
MA0025.10.487069
MA0027.11.90579
MA0028.10.027018
MA0029.10.308904
MA0030.10.300221
MA0031.10.703934
MA0038.10.126016
MA0040.10.313366
MA0041.10.0839596
MA0042.10.070122
MA0043.10.376179
MA0046.10.367181
MA0048.10.000441415
MA0050.10.0704881
MA0051.10.12372
MA0052.10.316327
MA0055.10.00401726
MA0056.10
MA0057.11.53968
MA0058.11.00687
MA0059.11.00159
MA0060.10.00534716
MA0061.10.0199515
MA0063.10
MA0066.10.126249
MA0067.11.56551
MA0068.10.921806
MA0069.10.364099
MA0070.10.355189
MA0071.12.30675
MA0072.11.65709
MA0073.132.4812
MA0074.10.123313
MA0076.11.07237
MA0077.10.345539
MA0078.10.182227
MA0081.10.0400838
MA0083.10.381987
MA0084.10.823032
MA0087.10.349692
MA0088.10.370125
MA0089.10
MA0090.10.0504181
MA0091.10.561757
MA0092.15.80795
MA0093.11.98377
MA0095.10
MA0098.10
MA0100.14.12815
MA0101.10.0246931
MA0103.10.0212236
MA0105.10.0089638
MA0106.10.14939
MA0107.10.011011
MA0108.20.69888
MA0109.10
MA0111.10.055257
MA0113.12.13815
MA0114.10.286723
MA0115.10.581155
MA0116.10.0115061
MA0117.11.04791
MA0119.11.34171
MA0122.11.91981
MA0124.10.544476
MA0125.10.471774
MA0130.10
MA0131.12.39821
MA0132.10
MA0133.10
MA0135.10.400588
MA0136.12.56692
MA0139.10.837938
MA0140.10.104326
MA0141.10.355203
MA0142.10.230443
MA0143.10.159255
MA0144.10.122937
MA0145.11.51878
MA0146.15.7165
MA0147.10.314268
MA0148.10.0868592
MA0149.10.0995233
MA0062.20.00301306
MA0035.20.103973
MA0039.22.58349
MA0138.20.183007
MA0002.20.503296
MA0137.20.0286334
MA0104.20.0879339
MA0047.20.142334
MA0112.21.6991
MA0065.22.52186
MA0150.10.0483839
MA0151.10
MA0152.10.107647
MA0153.10.457467
MA0154.10.00191347
MA0155.13.26224
MA0156.10.120803
MA0157.10.211768
MA0158.10
MA0159.10.0121148
MA0160.10.0939956
MA0161.10
MA0162.10.130474
MA0163.10.371453
MA0164.10.166704
MA0080.21.52474
MA0018.20.896155
MA0099.20.107829
MA0079.216.4201
MA0102.20.858102
MA0258.10.0390558
MA0259.10.561281
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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