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Coexpression cluster:C907: Difference between revisions

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{{Coexpression_clusters
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.0185447,0.631734,0.011703,0.0175751,0.00114007,0.255282,5.76662e-08,0.0428766,0.502814,0.260932,0.236266,0.0011761,2.79296e-05,0.404852,0.613018,4.25058e-09,0.00290512,5.10055e-08,0.530083,3.24047e-05,0.401506,0.000939223,0.582826,0.0331568,0.153513|tfbs_overrepresentation_for_novel_motifs=1.51683,0.0494815,0.823567,0.440628,0.267236,0.439064,0.511871,0.164003,0.94513,0.527834,0.410439,0.553754,0.127813,0.500805,0.266007,0.782718,0.728104,0.218596,0.137566,0.216842,0.305279,0.0355541,0.431698,0.262652,0.347482,0.575764,0.112018,3.90942,2.92264,0.329945,0.389837,0.764231,0.190489,0.129565,0.23642,0.452714,8.57625,0.440165,0.213144,0.14756,0.663028,0.97787,0.654894,0.264644,0.149259,0.333541,0.51292,0.4002,0.0372068,0.270138,0.589559,0.524278,0.0739421,0.839846,0.99088,0.503626,0.273964,0.472204,0.100358,0.47124,0.804523,1.28186,0.162346,0.700946,1.31866,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.973072,4.56924,0.988898,8.49201,0.114787,0.342172,0.684401,0.750836,0.341765,1.99757,0.699894,0.532172,0.166331,0.937974,2.09469,0.0591186,0.096982,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.207949,0.136404,0.82268,0.619373,0.0858425,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,1.64174,0.252953,0.315525,0.814459,0.300169,0.41935,1.12352,1.22295,12.326,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,3.07834,1.02292,1.77429,0.911957,2.6976,1.03718,0.539846,1.18405,0.0922077,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,2.59767,0.193834,3.01036,8.03203,3.47342,2.10954,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.183544,0.510589,6.47902|tfbs_overrepresentation_jaspar=MA0003.1;1.0633,MA0004.1;0.415381,MA0006.1;2.07537,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;3.79854,MA0017.1;2.25785,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;1.40203,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;2.55829,MA0050.1;0.403421,MA0051.1;1.27173,MA0052.1;0.795605,MA0055.1;0.0199484,MA0056.1;0,MA0057.1;0.0725989,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;0.162248,MA0061.1;0.139804,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.109867,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;1.21679,MA0074.1;3.23534,MA0076.1;0.339975,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;0.650888,MA0089.1;0,MA0090.1;1.66392,MA0091.1;1.07263,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.271368,MA0103.1;0.257174,MA0105.1;0.0643619,MA0106.1;0.554855,MA0107.1;0.205358,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;1.73095,MA0115.1;1.11137,MA0116.1;1.13131,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;2.42824,MA0125.1;0.986127,MA0130.1;0,MA0131.1;2.56981,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;0.474342,MA0141.1;4.23295,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;1.0529,MA0145.1;1.53859,MA0146.1;0.51271,MA0147.1;0.211483,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;10.0784,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.28622,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;8.33117,MA0065.2;1.10761,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.488402,MA0155.1;0.359913,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;2.00748,MA0161.1;0,MA0162.1;3.32001,MA0163.1;0.034916,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;11.3195,MA0102.2;1.41188,MA0258.1;1.61512,MA0259.1;5.22633,MA0442.1;0}}
|full_id=C907_Adipocyte_aorta_Smooth_Hepatic_Fibroblast_spleen_Mesenchymal
|id=C907
}}

Latest revision as of 11:33, 17 September 2013


Full id: C907_Adipocyte_aorta_Smooth_Hepatic_Fibroblast_spleen_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr14:92413867..92413880,-p11@FBLN5
Hg19::chr14:92413889..92413894,-p19@FBLN5
Hg19::chr14:92413896..92413917,-p10@FBLN5
Hg19::chr14:92413918..92413933,-p5@FBLN5
Hg19::chr14:92413955..92413970,-p6@FBLN5
Hg19::chr14:92413978..92413995,-p8@FBLN5
Hg19::chr14:92413998..92414054,-p3@FBLN5
Hg19::chr14:92414055..92414065,-p15@FBLN5
Hg19::chr14:92414271..92414293,-p21@FBLN5


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>

Cell Type
Ontology termp-valuen
fibroblast2.68e-1876
muscle precursor cell4.62e-1158
myoblast4.62e-1158
multi-potent skeletal muscle stem cell4.62e-1158
fat cell1.62e-1015
muscle cell8.05e-1055
contractile cell1.14e-0959
electrically responsive cell2.64e-0861
electrically active cell2.64e-0861
smooth muscle cell5.40e-0843
smooth muscle myoblast5.40e-0843
preadipocyte7.38e-0812
skin fibroblast9.85e-0723
Uber Anatomy
Ontology termp-valuen
adult organism2.18e-17114
muscle tissue1.62e-1364
musculature1.62e-1364
musculature of body1.62e-1364
dense mesenchyme tissue2.48e-1373
paraxial mesoderm4.03e-1372
presumptive paraxial mesoderm4.03e-1372
somite5.27e-1371
presomitic mesoderm5.27e-1371
presumptive segmental plate5.27e-1371
dermomyotome5.27e-1371
trunk paraxial mesoderm5.27e-1371
multi-tissue structure7.12e-13342
skeletal muscle tissue1.16e-1262
striated muscle tissue1.16e-1262
myotome1.16e-1262
tissue1.58e-10773
epithelial vesicle1.77e-1078
multi-cellular organism1.20e-09656
trunk mesenchyme1.39e-09122
multilaminar epithelium1.41e-0983
organism subdivision3.24e-09264
mesenchyme4.10e-09160
entire embryonic mesenchyme4.10e-09160
adipose tissue1.54e-0814
primary circulatory organ1.04e-0727
trunk2.33e-07199
anatomical cluster2.50e-07373
cell layer6.25e-07309
anatomical system7.25e-07624
anatomical group9.56e-07625


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)
MA0003.11.0633
MA0004.10.415381
MA0006.12.07537
MA0007.10.397529
MA0009.10.870971
MA0014.13.79854
MA0017.12.25785
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.11.40203
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.12.55829
MA0050.10.403421
MA0051.11.27173
MA0052.10.795605
MA0055.10.0199484
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.11.21679
MA0074.13.23534
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.650888
MA0089.10
MA0090.11.66392
MA0091.11.07263
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.11.73095
MA0115.11.11137
MA0116.11.13131
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.12.42824
MA0125.10.986127
MA0130.10
MA0131.12.56981
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.14.23295
MA0142.10.679161
MA0143.10.571113
MA0144.11.0529
MA0145.11.53859
MA0146.10.51271
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.210.0784
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.28.33117
MA0065.21.10761
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.488402
MA0155.10.359913
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.12.00748
MA0161.10
MA0162.13.32001
MA0163.10.034916
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.211.3195
MA0102.21.41188
MA0258.11.61512
MA0259.15.22633
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
E2F1#186984.36212374655942.18983367577486e-050.000481077070391777
POLR2A#543081.908847268051620.0116612289598830.0425834647322104
STAT1#677236.902195832399730.007591561082166650.0312886759218786



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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