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Coexpression cluster:C948: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.83884,0.0494815,0.305225,1.12193,0.267236,0.439064,0.511871,0.492582,0.161941,0.0287394,0.410439,0.553754,1.30067,0.500805,0.266007,0.782718,0.728104,0.624077,0.137566,0.0599474,0.305279,0.141777,0.431698,0.726652,0.347482,0.575764,0.36063,0.429643,0.270022,0.10044,0.389837,0.764231,0.557092,0.129565,0.23642,0.126309,1.22823,0.440165,0.213144,0.14756,0.663028,0.374544,0.0412835,0.731232,0.0550925,0.887061,0.51292,0.4002,0.0372068,0.270138,0.589559,1.30117,0.257164,0.839846,0.99088,0.503626,0.752594,0.472204,0.329728,0.47124,0.804523,0.5152,0.488493,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.0724994,0.988898,0.784625,0.367887,1.15181,0.684401,0.750836,0.341765,0.436045,0.699894,0.532172,0.166331,0.937974,0.0150019,0.214403,0.096982,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.207949,0.423564,0.82268,0.619373,0.606171,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,0.814459,1.47428,0.41935,2.5369,0.656078,0.0867932,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.0922077,0.999117,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.193834,0.50389,0.0382049,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.865335,0.673453,0.531409,0.540317,0.510589,0.0121205
|tfbs_overrepresentation_for_novel_motifs=0.83884,0.0494815,0.305225,1.12193,0.267236,0.439064,0.511871,0.492582,0.161941,0.0287394,0.410439,0.553754,1.30067,0.500805,0.266007,0.782718,0.728104,0.624077,0.137566,0.0599474,0.305279,0.141777,0.431698,0.726652,0.347482,0.575764,0.36063,0.429643,0.270022,0.10044,0.389837,0.764231,0.557092,0.129565,0.23642,0.126309,1.22823,0.440165,0.213144,0.14756,0.663028,0.374544,0.0412835,0.731232,0.0550925,0.887061,0.51292,0.4002,0.0372068,0.270138,0.589559,1.30117,0.257164,0.839846,0.99088,0.503626,0.752594,0.472204,0.329728,0.47124,0.804523,0.5152,0.488493,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.0724994,0.988898,0.784625,0.367887,1.15181,0.684401,0.750836,0.341765,0.436045,0.699894,0.532172,0.166331,0.937974,0.0150019,0.214403,0.096982,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.207949,0.423564,0.82268,0.619373,0.606171,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,0.814459,1.47428,0.41935,2.5369,0.656078,0.0867932,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.0922077,0.999117,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.193834,0.50389,0.0382049,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.865335,0.673453,0.531409,0.540317,0.510589,0.0121205
|tfbs_overrepresentation_jaspar=MA0003.1;0.169975,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;2.35363,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;0.280275,MA0029.1;1.84783,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;1.10579,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;0.264106,MA0050.1;1.04113,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;0.0199484,MA0056.1;0,MA0057.1;0.253359,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;3.19635e-05,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;0.650888,MA0089.1;0,MA0090.1;0.931587,MA0091.1;0.417885,MA0092.1;1.76221,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.271368,MA0103.1;1.31682,MA0105.1;0.229733,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;0.208403,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;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;3.43894,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;0.474342,MA0141.1;2.35992,MA0142.1;0.679161,MA0143.1;1.40034,MA0144.1;0.1885,MA0145.1;0.046841,MA0146.1;0.0260584,MA0147.1;0.211483,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;0.0189957,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.28622,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;0.166662,MA0065.2;0.0483532,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;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.0107891,MA0163.1;0.034916,MA0164.1;1.42569,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;2.07833e-05,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.218904,MA0442.1;0
}}
}}

Revision as of 19:34, 22 January 2013


Full id: C948_Adipocyte_Fibroblast_Preadipocyte_Ewing_normal_Smooth_Olfactory



Phase1 CAGE Peaks

Hg19::chr4:57897237..57897254,+p@chr4:57897237..57897254
+
Hg19::chr4:57897303..57897337,+p@chr4:57897303..57897337
+
Hg19::chr4:57898595..57898604,+p@chr4:57898595..57898604
+
Hg19::chr4:57898638..57898666,+p@chr4:57898638..57898666
+
Hg19::chr4:57899443..57899455,+p@chr4:57899443..57899455
+
Hg19::chr4:57906983..57906995,+p@chr4:57906983..57906995
+
Hg19::chr4:57907002..57907043,+p@chr4:57907002..57907043
+
Hg19::chr4:57976037..57976100,+p2@ENST00000508328
Hg19::chr4:57976101..57976199,+p1@ENST00000508328


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
epithelial tube9.84e-17117
vasculature1.33e-1678
vascular system1.33e-1678
splanchnic layer of lateral plate mesoderm1.77e-1583
cardiovascular system2.75e-14109
circulatory system3.08e-14112
vessel1.03e-1368
epithelial tube open at both ends3.20e-1259
blood vessel3.20e-1259
blood vasculature3.20e-1259
vascular cord3.20e-1259
artery6.45e-1142
arterial blood vessel6.45e-1142
arterial system6.45e-1142
anatomical cluster3.53e-09373
mesenchyme9.58e-09160
entire embryonic mesenchyme9.58e-09160
muscle tissue1.81e-0864
musculature1.81e-0864
musculature of body1.81e-0864
trunk2.35e-08199
epithelial vesicle2.82e-0878
heart3.04e-0824
primitive heart tube3.04e-0824
primary heart field3.04e-0824
anterior lateral plate mesoderm3.04e-0824
heart tube3.04e-0824
heart primordium3.04e-0824
cardiac mesoderm3.04e-0824
cardiogenic plate3.04e-0824
heart rudiment3.04e-0824
skeletal muscle tissue3.46e-0862
striated muscle tissue3.46e-0862
myotome3.46e-0862
compound organ4.49e-0868
organism subdivision5.98e-08264
primary circulatory organ7.37e-0827
anatomical conduit9.06e-08240
trunk mesenchyme1.70e-07122
systemic artery1.92e-0733
systemic arterial system1.92e-0733
body cavity precursor2.40e-0754
excretory tube2.78e-0716
kidney epithelium2.78e-0716
multilaminar epithelium4.59e-0783
nephron epithelium7.92e-0715
renal tubule7.92e-0715
nephron tubule7.92e-0715
nephron7.92e-0715
uriniferous tubule7.92e-0715
nephrogenic mesenchyme7.92e-0715
multi-tissue structure8.77e-07342
Disease
Ontology termp-valuen
ovarian cancer8.00e-0914


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)
MA0003.10.169975
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.0324647
MA0017.10.301634
MA0019.12.35363
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.11.84783
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.11.10579
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.264106
MA0050.11.04113
MA0051.10.510444
MA0052.10.795605
MA0055.10.0199484
MA0056.10
MA0057.10.253359
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
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.650888
MA0089.10
MA0090.10.931587
MA0091.10.417885
MA0092.11.76221
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.11.31682
MA0105.10.229733
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.12.42824
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.13.43894
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.12.35992
MA0142.10.679161
MA0143.11.40034
MA0144.10.1885
MA0145.10.046841
MA0146.10.0260584
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0189957
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.166662
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.156896
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.034916
MA0164.11.42569
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.22.07833e-05
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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