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Coexpression cluster:C952: Difference between revisions

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{{Coexpression_clusters
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539,0.637365,0.554869,0.692656,0.308763,0.521884,0.532407,0.307503,0.478305,0.470512,0.629431,0.263855,0.578048,0.41706,0.177548,0.255282,0.696023,0.53587,0.502814,0.260932,0.236266,0.6812,0.431685,0.404852,0.613018,0.198522,0.0707484,0.273479,0.530083,0.44039,0.401506,0.0377529,0.21811,0.499348,0.739615|tfbs_overrepresentation_for_novel_motifs=0.83884,2.71781,0.305225,0.440628,1.35412,0.439064,0.511871,0.164003,0.94513,0.527834,1.05643,0.553754,0.40163,0.500805,0.266007,0.287179,0.728104,0.218596,0.426514,0.0599474,0.305279,0.0355541,1.9325,2.06023,0.347482,2.40927,0.112018,1.09816,0.270022,1.1206,1.78971,0.764231,0.190489,1.31175,0.23642,0.00883671,0.233607,1.12093,0.213144,0.14756,0.235191,0.374544,1.44736,0.264644,0.781461,0.887061,1.277,0.4002,0.615516,0.270138,0.589559,0.524278,0.929597,0.839846,0.99088,0.503626,0.273964,0.472204,0.100358,0.47124,0.804523,0.5152,0.162346,2.81094,1.31866,0.667267,1.07848,1.44489,0.754027,1.28328,0.950736,0.168734,0.253077,0.988898,0.124338,0.114787,0.105027,0.684401,0.750836,0.905375,0.141333,0.699894,0.532172,0.166331,0.937974,0.358653,0.0591186,0.096982,0.614883,3.38479,1.17124,0.911274,0.78075,0.196636,1.35659,0.207949,0.423564,0.82268,0.619373,6.54422,0.214313,0.775192,3.17713,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,0.814459,0.300169,0.41935,1.12352,0.232218,1.82814,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.307751,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,2.04156,0.641461,1.83907,0.37143,0.193834,0.0656964,0.347165,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.540317,0.510589,0.196603|tfbs_overrepresentation_jaspar=MA0003.1;5.51661,MA0004.1;0.415381,MA0006.1;0.265592,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;1.50001,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;0.710608,MA0038.1;1.28049,MA0040.1;1.8598,MA0041.1;0.433167,MA0042.1;1.03929,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;1.95759,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;1.40898,MA0056.1;0,MA0057.1;0.253359,MA0058.1;0.325084,MA0059.1;0.865474,MA0060.1;0.488252,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;5.574,MA0074.1;0.509711,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;0.363555,MA0089.1;0,MA0090.1;0.353576,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;0.714036,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;0.200901,MA0115.1;1.11137,MA0116.1;0.599942,MA0117.1;0.908433,MA0119.1;1.50574,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;7.64524,MA0140.1;0.474342,MA0141.1;0.322254,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.1885,MA0145.1;6.84782,MA0146.1;0.0794051,MA0147.1;0.607251,MA0148.1;1.11902,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;2.14461,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.28622,MA0104.2;0.486672,MA0047.2;1.34084,MA0112.2;1.48222,MA0065.2;4.6152,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.062786,MA0155.1;8.15414,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.767014,MA0163.1;10.5556,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;8.9318,MA0102.2;1.41188,MA0258.1;0.532421,MA0259.1;0.624802,MA0442.1;0}}
|full_id=C952_basal_Fibroblast_tenocyte_Hair_Smooth_Preadipocyte_Myoblast
|id=C952
}}

Latest revision as of 11:34, 17 September 2013


Full id: C952_basal_Fibroblast_tenocyte_Hair_Smooth_Preadipocyte_Myoblast



Phase1 CAGE Peaks

Hg19::chr5:98104978..98105010,+p5@RGMB
Hg19::chr5:98105021..98105033,+p11@RGMB
Hg19::chr5:98105080..98105096,+p9@RGMB
Hg19::chr5:98105123..98105126,+p26@RGMB
Hg19::chr5:98105127..98105145,+p8@RGMB
Hg19::chr5:98105219..98105258,+p6@RGMB
Hg19::chr5:98105268..98105295,+p2@RGMB
Hg19::chr5:98105586..98105654,+p@chr5:98105586..98105654
+
Hg19::chr5:98109470..98109495,+p3@RGMB


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
dense mesenchyme tissue2.25e-2273
paraxial mesoderm7.75e-2272
presumptive paraxial mesoderm7.75e-2272
somite1.02e-2171
presomitic mesoderm1.02e-2171
presumptive segmental plate1.02e-2171
dermomyotome1.02e-2171
trunk paraxial mesoderm1.02e-2171
multilaminar epithelium1.19e-2083
epithelial vesicle1.53e-1978
cell layer2.80e-19309
epithelium5.26e-19306
artery1.46e-1742
arterial blood vessel1.46e-1742
arterial system1.46e-1742
muscle tissue3.22e-1764
musculature3.22e-1764
musculature of body3.22e-1764
skeletal muscle tissue4.58e-1762
striated muscle tissue4.58e-1762
myotome4.58e-1762
integument5.77e-1646
integumental system5.77e-1646
epithelial tube open at both ends2.82e-1559
blood vessel2.82e-1559
blood vasculature2.82e-1559
vascular cord2.82e-1559
vasculature3.87e-1578
vascular system3.87e-1578
skin of body4.32e-1541
vessel8.71e-1568
systemic artery1.34e-1433
systemic arterial system1.34e-1433
multi-tissue structure2.16e-14342
unilaminar epithelium3.08e-14148
surface structure3.33e-1499
anatomical system1.25e-13624
multi-cellular organism1.81e-13656
anatomical group1.88e-13625
anatomical cluster2.12e-13373
splanchnic layer of lateral plate mesoderm2.53e-1383
trunk mesenchyme2.30e-11122
mesenchyme8.93e-11160
entire embryonic mesenchyme8.93e-11160
structure with developmental contribution from neural crest2.09e-10132
anatomical conduit3.43e-10240
organism subdivision8.34e-10264
cardiovascular system1.40e-09109
tube1.44e-09192
circulatory system6.88e-09112
aorta2.79e-0821
aortic system2.79e-0821
epithelial tube5.59e-08117
trunk1.27e-07199
ectoderm-derived structure2.64e-07171
ectoderm2.64e-07171
presumptive ectoderm2.64e-07171
embryo4.02e-07592


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)
MA0003.15.51661
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.11.50001
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.11.28049
MA0040.11.8598
MA0041.10.433167
MA0042.11.03929
MA0043.10.871285
MA0046.10.860127
MA0048.11.95759
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.40898
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.865474
MA0060.10.488252
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
MA0073.15.574
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.714036
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.11.50574
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.17.64524
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.16.84782
MA0146.10.0794051
MA0147.10.607251
MA0148.11.11902
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.22.14461
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.486672
MA0047.21.34084
MA0112.21.48222
MA0065.24.6152
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.18.15414
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.767014
MA0163.110.5556
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.28.9318
MA0102.21.41188
MA0258.10.532421
MA0259.10.624802
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
CTCF#1066484.764672331622251.10088565904027e-050.000285157235477447
EGR1#195873.8796948515190.0003186557858542290.00326307398949209
RAD21#588578.053915252021592.36147727378579e-068.3802353040066e-05
ZBTB7A#5134175.718151683903472.40589727322203e-050.000524352056172862



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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