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Coexpression cluster:C423: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.274104,0.0280497,0.0765276,0.471537,0.212185,0.154482,0.204171,0.700835,0.422589,0.0680542,0.423075,0.23459,0.0561986,0.196345,0.210549,0.239229,0.372343,0.34735,0.33879,0.332863,0.264528,0.0935596,0.457087,0.2061,0.325988,0.251049,0.122351,0.453775,0.215908,0.875098,0.123558,0.402677,0.0283618,0.528541,0.172304,0.00981064,0.16879,0.155199,0.334646,0.073822,0.686612,0.114449,0.504679,0.458076,0.2886,0.0913173,0.591648,0.129869,1.11625,0.216063,0.261519,0.213054,0.259797,0.467708,0.602614,0.198331,0.0614355,0.523348,0.21737,0.175903,0.437087,0.595519,0.424001,0.349892,0.21901,0.32251,0.683218,1.032,0.394058,0.876356,0.107303,0.44639,0.253122,0.600809,0.502651,0.127377,0.915445,0.336375,0.39137,1.08854,0.881217,0.92151,0.624468,0.230083,0.554704,0.0242324,0.503719,0.36892,0.76873,1.1284,0.769994,0.530777,1.07009,0.545807,0.213076,1.32468,0.848106,0.452776,0.776697,0.173006,0.145304,0.41198,1.98755,0.375338,0.313482,0.133549,0.36244,0.194019,0.668456,0.0520752,0.279145,0.445659,0.0739965,0.141815,0.725188,0.675638,0.0371499,0.122878,0.858287,0.0312352,0.593343,0.279196,0.906976,0.643176,0.828974,0.33698,0.199838,0.420907,0.631927,0.13877,0.531386,0.125187,0.645033,0.224354,1.83983,0.802268,0.381933,0.454639,0.742365,1.57584,1.1795,0.707679,1.10241,0.449766,0.314855,0.509971,0.301898,1.41836,0.732167,0.290478,0.115484,0.048299,0.531723,0.400063,0.594726,0.90553,0.268853,0.195716,0.0989932,0.286826,0.706553,0.515425,1.79274,0.0861239,0.3275,0.218208,0.267508,1.11122,0.226929
|tfbs_overrepresentation_jaspar=MA0003.1;0.26005,MA0004.1;0.849835,MA0006.1;0.0576274,MA0007.1;0.128232,MA0009.1;0.495012,MA0014.1;0.0125068,MA0017.1;1.40092,MA0019.1;0.670127,MA0024.1;0.404839,MA0025.1;0.614568,MA0027.1;2.05626,MA0028.1;0.229764,MA0029.1;0.421158,MA0030.1;1.05866,MA0031.1;0.357843,MA0038.1;0.206085,MA0040.1;0.426128,MA0041.1;0.459457,MA0042.1;1.91598,MA0043.1;0.495289,MA0046.1;0.485466,MA0048.1;0.14539,MA0050.1;0.131853,MA0051.1;0.203156,MA0052.1;1.09767,MA0055.1;0.143182,MA0056.1;0,MA0057.1;0.0582452,MA0058.1;0.610819,MA0059.1;1.02017,MA0060.1;0.0198514,MA0061.1;0.579485,MA0063.1;0,MA0066.1;0.206381,MA0067.1;0.78548,MA0068.1;0.431486,MA0069.1;0.482095,MA0070.1;0.472333,MA0071.1;0.179775,MA0072.1;0.468422,MA0073.1;0.110485,MA0074.1;0.202636,MA0076.1;0.314823,MA0077.1;0.461731,MA0078.1;0.275364,MA0081.1;1.02075,MA0083.1;0.501617,MA0084.1;0.964138,MA0087.1;0.466297,MA0088.1;0.499444,MA0089.1;0,MA0090.1;1.66607,MA0091.1;0.434924,MA0092.1;0.378282,MA0093.1;0.810084,MA0095.1;0,MA0098.1;0,MA0100.1;0.61748,MA0101.1;0.474698,MA0103.1;0.198896,MA0105.1;0.215925,MA0106.1;0.235406,MA0107.1;0.316679,MA0108.2;0.355343,MA0109.1;0,MA0111.1;0.354483,MA0113.1;0.247415,MA0114.1;1.7264,MA0115.1;1.69871,MA0116.1;0.138337,MA0117.1;0.528241,MA0119.1;0.0783963,MA0122.1;0.551352,MA0124.1;0.675302,MA0125.1;0.598285,MA0130.1;0,MA0131.1;0.289284,MA0132.1;0,MA0133.1;0,MA0135.1;0.521813,MA0136.1;0.211008,MA0139.1;0.0119363,MA0140.1;0.526893,MA0141.1;1.01397,MA0142.1;0.88389,MA0143.1;0.691772,MA0144.1;0.115718,MA0145.1;0.0261554,MA0146.1;0.112952,MA0147.1;0.599621,MA0148.1;0.469347,MA0149.1;0.17166,MA0062.2;0.16671,MA0035.2;0.177548,MA0039.2;0.00953748,MA0138.2;0.757929,MA0002.2;0.956051,MA0137.2;0.237908,MA0104.2;0.688778,MA0047.2;0.643013,MA0112.2;0.223605,MA0065.2;1.07579,MA0150.1;0.670482,MA0151.1;0,MA0152.1;0.537486,MA0153.1;0.583009,MA0154.1;0.764168,MA0155.1;0.492054,MA0156.1;0.0681959,MA0157.1;0.310364,MA0158.1;0,MA0159.1;0.332094,MA0160.1;0.493256,MA0161.1;0,MA0162.1;0.00490328,MA0163.1;0.0599298,MA0164.1;0.256631,MA0080.2;0.21379,MA0018.2;0.236412,MA0099.2;0.538063,MA0079.2;0.00211511,MA0102.2;1.00004,MA0258.1;0.487257,MA0259.1;0.150791,MA0442.1;0
}}
}}

Revision as of 19:09, 22 January 2013


Full id: C423_Preadipocyte_Adipocyte_Chondrocyte_tenocyte_Osteoblast_Synoviocyte_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:114162377..114162406,+p@chr11:114162377..114162406
+
Hg19::chr11:66811898..66811900,-p@chr11:66811898..66811900
-
Hg19::chr11:86206996..86207000,+p@chr11:86206996..86207000
+
Hg19::chr12:130751497..130751499,+p@chr12:130751497..130751499
+
Hg19::chr15:68655558..68655569,-p@chr15:68655558..68655569
-
Hg19::chr15:68805087..68805101,+p@chr15:68805087..68805101
+
Hg19::chr16:28874345..28874371,+p8@SH2B1
Hg19::chr17:79402524..79402529,-p@chr17:79402524..79402529
-
Hg19::chr19:18893611..18893635,-p1@AK094919
Hg19::chr19:18901074..18901086,+p@chr19:18901074..18901086
+
Hg19::chr19:18902106..18902122,-p1@COMP
Hg19::chr1:103471622..103471650,+p@chr1:103471622..103471650
+
Hg19::chr1:240577171..240577181,-p@chr1:240577171..240577181
-
Hg19::chr1:3603926..3603929,+p@chr1:3603926..3603929
+
Hg19::chr22:44140357..44140361,+p@chr22:44140357..44140361
+
Hg19::chr2:30523559..30523563,-p@chr2:30523559..30523563
-
Hg19::chr4:815301..815303,-p@chr4:815301..815303
-
Hg19::chr5:125759509..125759522,+p@chr5:125759509..125759522
+
Hg19::chr5:35771474..35771476,+p@chr5:35771474..35771476
+
Hg19::chr6:75474615..75474618,+p@chr6:75474615..75474618
+
Hg19::chr6:75794245..75794256,-p12@AL359627
Hg19::chr6:75794482..75794491,-p19@AL359627
Hg19::chr6:75808553..75808557,-p@chr6:75808553..75808557
-
Hg19::chr7:150870947..150870948,+p@chr7:150870947..150870948
+


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:0005201extracellular matrix structural constituent0.00494503066961316
GO:0005595collagen type XII0.00494503066961316
GO:0001501skeletal development0.00494503066961316
GO:0030020extracellular matrix structural constituent conferring tensile strength0.00494503066961316
GO:0008140cAMP response element binding protein binding0.00593377478302222
GO:0005593FACIT collagen0.00988831463864661
GO:0005578proteinaceous extracellular matrix0.0108509110773683
GO:0030934anchoring collagen0.0109850757914487
GO:0030199collagen fibril organization0.0109850757914487
GO:0044421extracellular region part0.0318840616604973
GO:0022610biological adhesion0.0318840616604973
GO:0007155cell adhesion0.0318840616604973
GO:0005515protein binding0.0318840616604973
GO:0030198extracellular matrix organization and biogenesis0.0324328346247576
GO:0005581collagen0.0339362505987833
GO:0048513organ development0.0339362505987833
GO:0043062extracellular structure organization and biogenesis0.0486918785817363



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>

Cell Type
Ontology termp-valuen
preadipocyte of the breast8.55e-283
omentum preadipocyte9.40e-273
preadipocyte3.26e-2612
fat cell6.99e-2115
adipocyte of breast7.03e-192
fibroblast3.97e-1776
receptor cell3.03e-136
sensory epithelial cell3.03e-136
olfactory epithelial cell3.03e-136
skin fibroblast4.82e-1323
adipocyte of omentum tissue6.20e-133
Uber Anatomy
Ontology termp-valuen
omentum1.53e-366
peritoneum1.53e-366
abdominal cavity1.53e-366
visceral peritoneum1.53e-366
breast2.03e-2210
chest2.25e-2011
cavity lining2.93e-1812
serous membrane2.93e-1812
skin of body4.07e-0741
Disease
Ontology termp-valuen
musculoskeletal system disease9.55e-085
myotonic disease9.55e-085
muscle tissue disease9.55e-085
myopathy9.55e-085
muscular disease9.55e-085
myotonic dystrophy9.55e-085


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)
MA0003.10.26005
MA0004.10.849835
MA0006.10.0576274
MA0007.10.128232
MA0009.10.495012
MA0014.10.0125068
MA0017.11.40092
MA0019.10.670127
MA0024.10.404839
MA0025.10.614568
MA0027.12.05626
MA0028.10.229764
MA0029.10.421158
MA0030.11.05866
MA0031.10.357843
MA0038.10.206085
MA0040.10.426128
MA0041.10.459457
MA0042.11.91598
MA0043.10.495289
MA0046.10.485466
MA0048.10.14539
MA0050.10.131853
MA0051.10.203156
MA0052.11.09767
MA0055.10.143182
MA0056.10
MA0057.10.0582452
MA0058.10.610819
MA0059.11.02017
MA0060.10.0198514
MA0061.10.579485
MA0063.10
MA0066.10.206381
MA0067.10.78548
MA0068.10.431486
MA0069.10.482095
MA0070.10.472333
MA0071.10.179775
MA0072.10.468422
MA0073.10.110485
MA0074.10.202636
MA0076.10.314823
MA0077.10.461731
MA0078.10.275364
MA0081.11.02075
MA0083.10.501617
MA0084.10.964138
MA0087.10.466297
MA0088.10.499444
MA0089.10
MA0090.11.66607
MA0091.10.434924
MA0092.10.378282
MA0093.10.810084
MA0095.10
MA0098.10
MA0100.10.61748
MA0101.10.474698
MA0103.10.198896
MA0105.10.215925
MA0106.10.235406
MA0107.10.316679
MA0108.20.355343
MA0109.10
MA0111.10.354483
MA0113.10.247415
MA0114.11.7264
MA0115.11.69871
MA0116.10.138337
MA0117.10.528241
MA0119.10.0783963
MA0122.10.551352
MA0124.10.675302
MA0125.10.598285
MA0130.10
MA0131.10.289284
MA0132.10
MA0133.10
MA0135.10.521813
MA0136.10.211008
MA0139.10.0119363
MA0140.10.526893
MA0141.11.01397
MA0142.10.88389
MA0143.10.691772
MA0144.10.115718
MA0145.10.0261554
MA0146.10.112952
MA0147.10.599621
MA0148.10.469347
MA0149.10.17166
MA0062.20.16671
MA0035.20.177548
MA0039.20.00953748
MA0138.20.757929
MA0002.20.956051
MA0137.20.237908
MA0104.20.688778
MA0047.20.643013
MA0112.20.223605
MA0065.21.07579
MA0150.10.670482
MA0151.10
MA0152.10.537486
MA0153.10.583009
MA0154.10.764168
MA0155.10.492054
MA0156.10.0681959
MA0157.10.310364
MA0158.10
MA0159.10.332094
MA0160.10.493256
MA0161.10
MA0162.10.00490328
MA0163.10.0599298
MA0164.10.256631
MA0080.20.21379
MA0018.20.236412
MA0099.20.538063
MA0079.20.00211511
MA0102.21.00004
MA0258.10.487257
MA0259.10.150791
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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