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Coexpression cluster:C382: Difference between revisions

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{{Coexpression_clusters
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.88628,0.609642,0.567665,0.475529,0.827615,0.801009,0.793816,0.497662,0.175585,0.629893,0.210792,0.835698,0.215881,0.194122,0.754926,0.633676,0.602053|tfbs_overrepresentation_for_novel_motifs=0.462305,0.13035,0.446636,0.122847,1.0076,0.386501,0.166546,0.156756,0.153215,0.0684611,0.105867,0.566381,0.858425,0.159448,1.00179,0.405555,0.323398,0.10615,0.0397851,0.21308,0.202659,0.0480554,0.117723,0.152436,0.0738203,0.209525,0.311283,0.116555,0.36738,0.141569,0.31494,0.352308,0.651307,0.101378,0.0302015,0.113304,0.28961,0.122579,0.0234283,0.0464435,0.539571,0.293556,0.0626908,0.154672,0.0955103,0.0673916,1.53976,1.64752,0.18135,0.160896,0.219219,0.174632,0.447734,0.414705,0.545525,0.161247,0.165281,0.436764,0.905995,0.14103,0.385258,0.50414,0.309783,0.302097,0.180069,1.38725,0.62433,0.968521,0.34408,0.814438,0.0808966,0.328843,0.436902,0.543765,0.0317128,0.0803588,1.26003,0.289314,3.37845,0.532397,1.29887,0.30128,0.179843,5.27972,0.49889,0.000781693,14.4667,0.0576074,0.237365,1.06421,0.709557,0.475666,0.36573,0.0855472,0.158355,1.07287,1.2521,1.03439,0.240628,0.764638,0.101994,0.361201,0.395756,0.326247,0.738351,0.103543,0.843302,0.476111,0.256507,0.141721,0.47048,0.39349,0.196387,0.357368,0.665507,0.28674,0.197017,0.0942716,0.274506,0.42254,0.536488,0.664105,0.120436,1.04739,1.8101,0.289886,0.489153,0.369745,0.574137,0.453425,0.476257,1.61016,0.586948,0.543744,0.721448,3.03895,0.0919419,0.373297,0.682384,1.50986,1.115,0.648318,0.491786,1.02807,0.741309,0.838665,0.256873,1.35281,0.0854457,0.406,0.0256312,0.023137,0.476584,0.142269,0.503396,0.843272,0.641569,0.143671,0.256891,0.0617651,0.647214,0.460792,0.340895,2.34197,0.28094,0.53011,0.373958,0.165719,0.000908368|tfbs_overrepresentation_jaspar=MA0003.1;0.000415013,MA0004.1;0.108579,MA0006.1;3.02382,MA0007.1;0.0989131,MA0009.1;0.441048,MA0014.1;0.0668357,MA0017.1;0.438391,MA0019.1;0.574419,MA0024.1;0.933353,MA0025.1;0.557187,MA0027.1;1.98963,MA0028.1;0.0452766,MA0029.1;2.59079,MA0030.1;0.947354,MA0031.1;0.309631,MA0038.1;0.503116,MA0040.1;0.374747,MA0041.1;1.24135,MA0042.1;0.333074,MA0043.1;0.441316,MA0046.1;0.431829,MA0048.1;0.0875469,MA0050.1;1.1317,MA0051.1;0.165625,MA0052.1;0.377904,MA0055.1;0.12662,MA0056.1;0,MA0057.1;0.079803,MA0058.1;0.0636171,MA0059.1;0.0630872,MA0060.1;0.309494,MA0061.1;0.116963,MA0063.1;0,MA0066.1;0.168556,MA0067.1;0.724802,MA0068.1;0.0737762,MA0069.1;0.428576,MA0070.1;0.419162,MA0071.1;0.144505,MA0072.1;0.415392,MA0073.1;0.00103994,MA0074.1;0.165153,MA0076.1;0.246894,MA0077.1;0.408948,MA0078.1;0.232083,MA0081.1;1.27859,MA0083.1;0.447432,MA0084.1;0.901266,MA0087.1;0.413345,MA0088.1;0.00889845,MA0089.1;0,MA0090.1;0.560778,MA0091.1;0.109964,MA0092.1;0.0907294,MA0093.1;0.0408902,MA0095.1;0,MA0098.1;0,MA0100.1;0.17714,MA0101.1;0.0419777,MA0103.1;0.146349,MA0105.1;0.0639277,MA0106.1;0.195103,MA0107.1;0.0935176,MA0108.2;0.828157,MA0109.1;0,MA0111.1;0.996677,MA0113.1;0.206168,MA0114.1;1.85465,MA0115.1;0.654355,MA0116.1;0.0221565,MA0117.1;0.473208,MA0119.1;1.20604,MA0122.1;0.495633,MA0124.1;0.616574,MA0125.1;0.541304,MA0130.1;0,MA0131.1;0.245067,MA0132.1;0,MA0133.1;0,MA0135.1;0.466979,MA0136.1;0.514095,MA0139.1;0.00650158,MA0140.1;0.142924,MA0141.1;0.0623757,MA0142.1;0.285297,MA0143.1;0.206288,MA0144.1;0.200729,MA0145.1;0.034782,MA0146.1;0.000177961,MA0147.1;0.0992838,MA0148.1;0.38682,MA0149.1;0.425665,MA0062.2;0.00728391,MA0035.2;0.142505,MA0039.2;0.0018833,MA0138.2;0.6578,MA0002.2;0.137341,MA0137.2;0.179602,MA0104.2;0.0565825,MA0047.2;1.04713,MA0112.2;0.131639,MA0065.2;1.27248,MA0150.1;0.257536,MA0151.1;0,MA0152.1;0.44991,MA0153.1;0.526421,MA0154.1;0.538302,MA0155.1;0.0599969,MA0156.1;0.0483557,MA0157.1;0.264816,MA0158.1;0,MA0159.1;0.245967,MA0160.1;0.130642,MA0161.1;0,MA0162.1;5.32685e-05,MA0163.1;0.010716,MA0164.1;0.614845,MA0080.2;0.363904,MA0018.2;0.196028,MA0099.2;0.147056,MA0079.2;0.000141406,MA0102.2;0.936833,MA0258.1;0.0714019,MA0259.1;0.025023,MA0442.1;0}}
|full_id=C382_dura_Preadipocyte_Adipocyte_Astrocyte_trachea_diaphragm_vein
|id=C382
}}

Latest revision as of 11:21, 17 September 2013


Full id: C382_dura_Preadipocyte_Adipocyte_Astrocyte_trachea_diaphragm_vein



Phase1 CAGE Peaks

Hg19::chr10:78078199..78078208,+p8@C10orf11
Hg19::chr10:79398656..79398666,-p25@KCNMA1
Hg19::chr1:110626157..110626165,+p@chr1:110626157..110626165
+
Hg19::chr2:217560615..217560623,-p73@IGFBP5
Hg19::chr2:45234395..45234400,-p@chr2:45234395..45234400
-
Hg19::chr2:45715445..45715482,-p@chr2:45715445..45715482
-
Hg19::chr3:112931366..112931373,-p@chr3:112931366..112931373
-
Hg19::chr3:112931383..112931390,-p@chr3:112931383..112931390
-
Hg19::chr3:112931404..112931414,-p@chr3:112931404..112931414
-
Hg19::chr3:112931435..112931445,-p@chr3:112931435..112931445
-
Hg19::chr3:112931478..112931524,-p@chr3:112931478..112931524
-
Hg19::chr3:112931527..112931557,-p@chr3:112931527..112931557
-
Hg19::chr4:154709612..154709627,+p@chr4:154709612..154709627
+
Hg19::chr4:154710210..154710243,-p1@SFRP2
Hg19::chr4:154711058..154711075,+p@chr4:154711058..154711075
+
Hg19::chr4:154712764..154712772,-p@chr4:154712764..154712772
-
Hg19::chr5:122434917..122434927,+p@chr5:122434917..122434927
+
Hg19::chr5:122434947..122434959,+p4@PRDM6
Hg19::chr5:39892092..39892099,+p@chr5:39892092..39892099
+
Hg19::chr5:39892121..39892134,+p@chr5:39892121..39892134
+
Hg19::chr7:115135068..115135092,-p@chr7:115135068..115135092
-
Hg19::chr8:43349758..43349771,+p@chr8:43349758..43349771
+
Hg19::chr8:43349794..43349803,+p@chr8:43349794..43349803
+
Hg19::chr8:43349847..43349852,+p@chr8:43349847..43349852
+
Hg19::chr8:48651813..48651830,-p14@CEBPD
Hg19::chr9:23524699..23524703,-p@chr9:23524699..23524703
-
Hg19::chr9:23524722..23524736,-p@chr9:23524722..23524736
-
Hg19::chr9:23524772..23524783,-p@chr9:23524772..23524783
-


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:0005515protein binding0.018939282072879
GO:0051150regulation of smooth muscle cell differentiation0.018939282072879
GO:0051151negative regulation of smooth muscle cell differentiation0.018939282072879
GO:0051148negative regulation of muscle cell differentiation0.018939282072879
GO:0051147regulation of muscle cell differentiation0.0202004141903781
GO:0051145smooth muscle cell differentiation0.0336574476799169
GO:0046983protein dimerization activity0.0344695852545456



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
dura mater9.37e-991
future meninx9.37e-991
ectomeninx9.37e-991
future dura mater9.37e-991
meninx2.74e-502
membrane organ2.74e-502
meningeal cluster2.74e-502
retina9.07e-186
photoreceptor array9.07e-186
posterior segment of eyeball9.07e-186


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)
MA0003.10.000415013
MA0004.10.108579
MA0006.13.02382
MA0007.10.0989131
MA0009.10.441048
MA0014.10.0668357
MA0017.10.438391
MA0019.10.574419
MA0024.10.933353
MA0025.10.557187
MA0027.11.98963
MA0028.10.0452766
MA0029.12.59079
MA0030.10.947354
MA0031.10.309631
MA0038.10.503116
MA0040.10.374747
MA0041.11.24135
MA0042.10.333074
MA0043.10.441316
MA0046.10.431829
MA0048.10.0875469
MA0050.11.1317
MA0051.10.165625
MA0052.10.377904
MA0055.10.12662
MA0056.10
MA0057.10.079803
MA0058.10.0636171
MA0059.10.0630872
MA0060.10.309494
MA0061.10.116963
MA0063.10
MA0066.10.168556
MA0067.10.724802
MA0068.10.0737762
MA0069.10.428576
MA0070.10.419162
MA0071.10.144505
MA0072.10.415392
MA0073.10.00103994
MA0074.10.165153
MA0076.10.246894
MA0077.10.408948
MA0078.10.232083
MA0081.11.27859
MA0083.10.447432
MA0084.10.901266
MA0087.10.413345
MA0088.10.00889845
MA0089.10
MA0090.10.560778
MA0091.10.109964
MA0092.10.0907294
MA0093.10.0408902
MA0095.10
MA0098.10
MA0100.10.17714
MA0101.10.0419777
MA0103.10.146349
MA0105.10.0639277
MA0106.10.195103
MA0107.10.0935176
MA0108.20.828157
MA0109.10
MA0111.10.996677
MA0113.10.206168
MA0114.11.85465
MA0115.10.654355
MA0116.10.0221565
MA0117.10.473208
MA0119.11.20604
MA0122.10.495633
MA0124.10.616574
MA0125.10.541304
MA0130.10
MA0131.10.245067
MA0132.10
MA0133.10
MA0135.10.466979
MA0136.10.514095
MA0139.10.00650158
MA0140.10.142924
MA0141.10.0623757
MA0142.10.285297
MA0143.10.206288
MA0144.10.200729
MA0145.10.034782
MA0146.10.000177961
MA0147.10.0992838
MA0148.10.38682
MA0149.10.425665
MA0062.20.00728391
MA0035.20.142505
MA0039.20.0018833
MA0138.20.6578
MA0002.20.137341
MA0137.20.179602
MA0104.20.0565825
MA0047.21.04713
MA0112.20.131639
MA0065.21.27248
MA0150.10.257536
MA0151.10
MA0152.10.44991
MA0153.10.526421
MA0154.10.538302
MA0155.10.0599969
MA0156.10.0483557
MA0157.10.264816
MA0158.10
MA0159.10.245967
MA0160.10.130642
MA0161.10
MA0162.15.32685e-05
MA0163.10.010716
MA0164.10.614845
MA0080.20.363904
MA0018.20.196028
MA0099.20.147056
MA0079.20.000141406
MA0102.20.936833
MA0258.10.0714019
MA0259.10.025023
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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