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Coexpression cluster:C558: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.157827,0.290484,0.152819,0.258928,0.395738,0.25764,0.318839,0.215354,0.463955,0.0627782,0.234283,0.355038,0.643012,0.309388,1.28063,0.851457,0.511522,1.06688,0.171822,0.791358,0.152859,1.38447,0.251588,0.387475,0.18461,0.374311,1.73859,0.697239,0.798464,0.815202,0.217756,0.544857,0.0750467,0.651427,0.340569,0.405974,0.102549,0.717201,0.299553,0.419472,0.338389,0.205653,0.852782,0.781844,0.90499,0.173971,0.319738,0.226038,0.339857,0.798822,0.386472,0.329494,0.377869,0.615394,0.758742,0.311792,0.810644,0.778218,0.814637,0.284391,0.582323,0.321692,1.22686,0.48664,0.893874,0.456015,0.843028,1.20113,0.535417,1.04233,0.19602,0.22329,0.0158491,0.756844,0.150647,1.3125,0.532449,0.471562,1.31856,0.18023,0.177931,0.48568,0.336303,0.0607686,0.70821,0.00751148,0.0112665,0.10849,0.408949,1.29895,0.932961,0.68283,0.560183,0.0788172,0.396944,0.0858933,0.385004,0.599297,0.412954,0.0920994,0.301599,0.555021,0.594155,0.514828,0.445845,0.230832,0.500571,0.826592,0.18443,0.115618,0.48378,0.591605,0.149112,0.241506,0.886618,0.333119,0.0385455,0.216858,0.453946,0.0803321,0.748992,0.406842,0.255485,0.345739,0.993708,0.472239,0.313614,0.564749,0.78949,0.0864157,0.683478,0.627156,0.803201,0.342946,0.945426,0.101403,0.21329,0.250344,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.278424,0.432737,1.59165,0.58757,0.0770919,0.850402,0.0298174,0.683836,0.201134,0.321292,1.07219,0.394947,0.751217,0.184652,0.164414,0.867287,0.66649,0.531753,0.499061,0.46162,0.335644,0.0708512,0.317742,0.198736
|tfbs_overrepresentation_jaspar=MA0003.1;0.038097,MA0004.1;1.24596,MA0006.1;0.784773,MA0007.1;0.636564,MA0009.1;0.644692,MA0014.1;0.193248,MA0017.1;0.89607,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.134741,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;0.252793,MA0042.1;0.227947,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.0786451,MA0050.1;0.228625,MA0051.1;0.317617,MA0052.1;0.574006,MA0055.1;0.970157,MA0056.1;0,MA0057.1;0.0733461,MA0058.1;0.968374,MA0059.1;1.53659,MA0060.1;0.0584466,MA0061.1;0.395503,MA0063.1;0,MA0066.1;1.55071,MA0067.1;0.948938,MA0068.1;0.128042,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;0.616162,MA0073.1;0.0057658,MA0074.1;0.316991,MA0076.1;0.178863,MA0077.1;0.608956,MA0078.1;0.402443,MA0081.1;0.166796,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.20753,MA0089.1;0,MA0090.1;0.189305,MA0091.1;0.240316,MA0092.1;0.211423,MA0093.1;1.29113,MA0095.1;0,MA0098.1;0,MA0100.1;0.332778,MA0101.1;0.128426,MA0103.1;1.24111,MA0105.1;0.836818,MA0106.1;0.355999,MA0107.1;0.598395,MA0108.2;0.492699,MA0109.1;0,MA0111.1;0.199239,MA0113.1;0.968027,MA0114.1;0.985949,MA0115.1;0.874839,MA0116.1;0.291279,MA0117.1;0.680135,MA0119.1;0.471628,MA0122.1;0.70466,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;0.418384,MA0132.1;0,MA0133.1;0,MA0135.1;0.673296,MA0136.1;0.327047,MA0139.1;0.652922,MA0140.1;0.286995,MA0141.1;1.52947,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.928804,MA0145.1;0.418252,MA0146.1;0.528155,MA0147.1;1.53356,MA0148.1;0.257816,MA0149.1;0.279141,MA0062.2;0.0439512,MA0035.2;0.286421,MA0039.2;0.143918,MA0138.2;1.04135,MA0002.2;0.434729,MA0137.2;0.430142,MA0104.2;1.70899,MA0047.2;0.345656,MA0112.2;2.87571,MA0065.2;0.430296,MA0150.1;0.185024,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;0.542249,MA0155.1;0.837529,MA0156.1;0.854962,MA0157.1;0.442323,MA0158.1;0,MA0159.1;0.0884959,MA0160.1;0.743405,MA0161.1;0,MA0162.1;0.311763,MA0163.1;0.324683,MA0164.1;0.99163,MA0080.2;0.126365,MA0018.2;0.357181,MA0099.2;0.292649,MA0079.2;0.0254531,MA0102.2;1.16862,MA0258.1;3.07274,MA0259.1;1.06828,MA0442.1;0
}}
}}

Revision as of 19:16, 22 January 2013


Full id: C558_Mesenchymal_testis_Smooth_Endothelial_Placental_Tracheal_Hair



Phase1 CAGE Peaks

Hg19::chr11:120317216..120317220,+p@chr11:120317216..120317220
+
Hg19::chr11:500479..500483,-p@chr11:500479..500483
-
Hg19::chr16:15128409..15128413,+p@chr16:15128409..15128413
+
Hg19::chr16:87400976..87400979,-p@chr16:87400976..87400979
-
Hg19::chr17:38324198..38324204,+p7@CASC3
Hg19::chr17:79873312..79873316,-p@chr17:79873312..79873316
-
Hg19::chr18:77096710..77096715,+p@chr18:77096710..77096715
+
Hg19::chr19:2353015..2353053,+p@chr19:2353015..2353053
+
Hg19::chr1:156893889..156893893,+p@chr1:156893889..156893893
+
Hg19::chr20:44582326..44582328,-p@chr20:44582326..44582328
-
Hg19::chr22:19376002..19376007,-p@chr22:19376002..19376007
-
Hg19::chr22:24431967..24431972,+p@chr22:24431967..24431972
+
Hg19::chr2:242607635..242607639,+p7@ATG4B
Hg19::chr3:49070544..49070558,-p8@QRICH1
Hg19::chr3:52381988..52381993,+p@chr3:52381988..52381993
+
Hg19::chr9:131864675..131864680,-p@chr9:131864675..131864680
-


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:0008298intracellular mRNA localization0.0135990345038516
GO:0000045autophagic vacuole formation0.0203943486750239
GO:0016236macroautophagy0.0203943486750239
GO:0006914autophagy0.0401466589318227
GO:0033036macromolecule localization0.0401466589318227
GO:0006612protein targeting to membrane0.0407562844025515



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
uterine smooth muscle cell1.12e-091
stromal cell of pancreas2.16e-091
Uber Anatomy
Ontology termp-valuen
cartilage tissue2.44e-113
skeletal tissue2.44e-113
Disease
Ontology termp-valuen
chondrosarcoma5.28e-091
extraosseous chondrosarcoma5.28e-091
myxoid chondrosarcoma5.28e-091
extraskeletal myxoid chondrosarcoma5.28e-091


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)
MA0003.10.038097
MA0004.11.24596
MA0006.10.784773
MA0007.10.636564
MA0009.10.644692
MA0014.10.193248
MA0017.10.89607
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.0786451
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.970157
MA0056.10
MA0057.10.0733461
MA0058.10.968374
MA0059.11.53659
MA0060.10.0584466
MA0061.10.395503
MA0063.10
MA0066.11.55071
MA0067.10.948938
MA0068.10.128042
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.0057658
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.166796
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.20753
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.10.211423
MA0093.11.29113
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.128426
MA0103.11.24111
MA0105.10.836818
MA0106.10.355999
MA0107.10.598395
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.968027
MA0114.10.985949
MA0115.10.874839
MA0116.10.291279
MA0117.10.680135
MA0119.10.471628
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.10.652922
MA0140.10.286995
MA0141.11.52947
MA0142.10.4668
MA0143.10.370225
MA0144.10.928804
MA0145.10.418252
MA0146.10.528155
MA0147.11.53356
MA0148.10.257816
MA0149.10.279141
MA0062.20.0439512
MA0035.20.286421
MA0039.20.143918
MA0138.21.04135
MA0002.20.434729
MA0137.20.430142
MA0104.21.70899
MA0047.20.345656
MA0112.22.87571
MA0065.20.430296
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.542249
MA0155.10.837529
MA0156.10.854962
MA0157.10.442323
MA0158.10
MA0159.10.0884959
MA0160.10.743405
MA0161.10
MA0162.10.311763
MA0163.10.324683
MA0164.10.99163
MA0080.20.126365
MA0018.20.357181
MA0099.20.292649
MA0079.20.0254531
MA0102.21.16862
MA0258.13.07274
MA0259.11.06828
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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