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Coexpression cluster:C960: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.312007,0.00986147,0.823567,0.440628,0.737182,0.439064,0.511871,0.164003,0.161941,0.285547,1.05643,0.553754,0.127813,0.500805,1.34958,1.42721,0.728104,1.17081,0.426514,0.216842,2.27601,0.33045,0.431698,0.726652,0.918075,0.575764,0.729404,0.429643,0.270022,0.329945,0.389837,0.764231,1.06082,0.129565,0.23642,0.69854,0.233607,0.440165,0.213144,0.14756,0.235191,0.374544,0.0412835,0.264644,0.0550925,0.333541,0.51292,1.0341,0.0372068,0.743836,0.589559,0.524278,0.546719,0.839846,0.99088,0.503626,0.273964,0.472204,0.67562,0.47124,0.804523,0.5152,0.488493,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.0724994,0.988898,0.124338,0.114787,0.105027,0.684401,0.750836,0.341765,0.436045,0.699894,0.532172,0.166331,0.937974,0.0150019,0.0591186,2.20785,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.207949,0.136404,0.82268,0.619373,0.0858425,0.214313,0.775192,1.91213,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.704291,0.315525,0.814459,0.300169,0.41935,1.12352,1.22295,0.0194997,0.388709,0.664981,1.72086,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.0922077,0.999117,0.430179,1.14186,1.99816,1.59626,1.10478,2.18551,1.91629,0.657732,1.17257,1.54804,1.83907,0.37143,0.193834,0.0656964,0.0382049,0.912334,0.155464,0.514733,1.31376,0.599133,0.708413,0.347536,0.320853,1.10357,0.894035,1.77373,0.323817,0.673453,1.31632,0.183544,0.510589,0.00185481
|tfbs_overrepresentation_for_novel_motifs=0.312007,0.00986147,0.823567,0.440628,0.737182,0.439064,0.511871,0.164003,0.161941,0.285547,1.05643,0.553754,0.127813,0.500805,1.34958,1.42721,0.728104,1.17081,0.426514,0.216842,2.27601,0.33045,0.431698,0.726652,0.918075,0.575764,0.729404,0.429643,0.270022,0.329945,0.389837,0.764231,1.06082,0.129565,0.23642,0.69854,0.233607,0.440165,0.213144,0.14756,0.235191,0.374544,0.0412835,0.264644,0.0550925,0.333541,0.51292,1.0341,0.0372068,0.743836,0.589559,0.524278,0.546719,0.839846,0.99088,0.503626,0.273964,0.472204,0.67562,0.47124,0.804523,0.5152,0.488493,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.0724994,0.988898,0.124338,0.114787,0.105027,0.684401,0.750836,0.341765,0.436045,0.699894,0.532172,0.166331,0.937974,0.0150019,0.0591186,2.20785,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.207949,0.136404,0.82268,0.619373,0.0858425,0.214313,0.775192,1.91213,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.704291,0.315525,0.814459,0.300169,0.41935,1.12352,1.22295,0.0194997,0.388709,0.664981,1.72086,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.0922077,0.999117,0.430179,1.14186,1.99816,1.59626,1.10478,2.18551,1.91629,0.657732,1.17257,1.54804,1.83907,0.37143,0.193834,0.0656964,0.0382049,0.912334,0.155464,0.514733,1.31376,0.599133,0.708413,0.347536,0.320853,1.10357,0.894035,1.77373,0.323817,0.673453,1.31632,0.183544,0.510589,0.00185481
|tfbs_overrepresentation_jaspar=MA0003.1;0.00371372,MA0004.1;0.415381,MA0006.1;0.265592,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.0324647,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;0.280275,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;1.69202,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;0.948258,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;13.279,MA0056.1;0,MA0057.1;0.919325,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;1.5106,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;0.0176541,MA0074.1;0.509711,MA0076.1;0.339975,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.865814,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;0.650888,MA0089.1;0,MA0090.1;0.931587,MA0091.1;0.417885,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;2.83198,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;0.200901,MA0115.1;1.11137,MA0116.1;0.208403,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;2.07572,MA0141.1;1.55341,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.1885,MA0145.1;0.046841,MA0146.1;0.0045741,MA0147.1;0.211483,MA0148.1;0.439278,MA0149.1;2.04443,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;0.0006485,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.28622,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;0.0433683,MA0065.2;0.719797,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.062786,MA0155.1;0.156896,MA0156.1;0.288314,MA0157.1;1.57029,MA0158.1;0,MA0159.1;0.212043,MA0160.1;1.15068,MA0161.1;0,MA0162.1;0.0533066,MA0163.1;0.034916,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;0.0681378,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.218904,MA0442.1;0
}}
}}

Revision as of 19:35, 22 January 2013


Full id: C960_Preadipocyte_giant_Smooth_Fibroblast_fibrous_mesenchymal_Meningeal



Phase1 CAGE Peaks

Hg19::chr8:23699989..23700003,-p2@STC1
Hg19::chr8:23700042..23700103,-p4@STC1
Hg19::chr8:23700304..23700316,-p7@STC1
Hg19::chr8:23700350..23700367,-p9@STC1
Hg19::chr8:23700484..23700506,-p6@STC1
Hg19::chr8:23700592..23700603,-p@chr8:23700592..23700603
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Hg19::chr8:23702223..23702240,-p@chr8:23702223..23702240
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Hg19::chr8:23702263..23702282,-p@chr8:23702263..23702282
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Hg19::chr8:23712312..23712328,-p1@STC1


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
somite4.51e-1171
presomitic mesoderm4.51e-1171
presumptive segmental plate4.51e-1171
dermomyotome4.51e-1171
trunk paraxial mesoderm4.51e-1171
artery1.00e-1042
arterial blood vessel1.00e-1042
arterial system1.00e-1042
paraxial mesoderm1.02e-1072
presumptive paraxial mesoderm1.02e-1072
systemic artery1.09e-1033
systemic arterial system1.09e-1033
dense mesenchyme tissue2.26e-1073
multilaminar epithelium1.34e-0983
skeletal muscle tissue1.83e-0962
striated muscle tissue1.83e-0962
myotome1.83e-0962
epithelial vesicle1.89e-0978
muscle tissue2.92e-0964
musculature2.92e-0964
musculature of body2.92e-0964
trunk mesenchyme6.61e-09122
blood vessel smooth muscle7.51e-0910
arterial system smooth muscle7.51e-0910
artery smooth muscle tissue7.51e-0910
aorta smooth muscle tissue7.51e-0910
female gonad1.28e-0713
reproductive structure1.90e-0759
reproductive system1.90e-0759
trunk2.08e-07199
female reproductive organ3.15e-0737
female reproductive system3.15e-0737
unilaminar epithelium4.00e-07148
epithelial tube open at both ends4.39e-0759
blood vessel4.39e-0759
blood vasculature4.39e-0759
vascular cord4.39e-0759
mesenchyme6.23e-07160
entire embryonic mesenchyme6.23e-07160
Disease
Ontology termp-valuen
ovarian cancer6.41e-1314
female reproductive organ cancer1.78e-0927
reproductive organ cancer2.57e-0829


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)
MA0003.10.00371372
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.0324647
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.11.69202
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.948258
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.113.279
MA0056.10
MA0057.10.919325
MA0058.10.325084
MA0059.10.323879
MA0060.11.5106
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
MA0073.10.0176541
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.865814
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.650888
MA0089.10
MA0090.10.931587
MA0091.10.417885
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
MA0108.22.83198
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.12.07572
MA0141.11.55341
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.0045741
MA0147.10.211483
MA0148.10.439278
MA0149.12.04443
MA0062.20.135498
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.719797
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.156896
MA0156.10.288314
MA0157.11.57029
MA0158.10
MA0159.10.212043
MA0160.11.15068
MA0161.10
MA0162.10.0533066
MA0163.10.034916
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.0681378
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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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