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Coexpression cluster:C1960: Difference between revisions

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{{Coexpression_clusters
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61,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.0275302,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.00268101,0.508546,0.224871,0.398887,0.389061,0.310732,0.349611,0.445995,0.0863731,0.278202,0.426488,0.400591,0.209809,0.253154,0.0071437,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.0494743,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=2.1885,4.86949,0.500341,1.57627,1.15291,0.653236,0.733342,0.324142,0.321368,0.106358,2.55627,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,2.18893,0.167776,0.500405,0.770467,1.55551,0.44943,0.549618,0.802434,0.700122,0.642741,0.458349,1.22891,0.598009,1.00172,0.359091,0.27659,0.417272,0.432883,0.413782,0.654459,0.388123,2.25858,0.415749,0.580638,0.821929,0.451846,1.25074,0.533483,0.734485,2.51915,0.785708,0.458489,0.817229,1.76707,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,1.74665,0.321912,2.15436,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,2.09345,2.02182,0.240727,3.49093,0.987729,0.543014,1.44891,0.934302,0.755403,0.327263,1.18161,1.89992,0.166306,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,1.15465,0.381528,0.28626,1.06255,0.849074,2.52127,0.389604,1.01316,2.40164,0.967698,2.05741,0.616433,0.951411,0.717647,1.35434,1.11542,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,1.49495,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,5.56588,1.02407,1.2687,0.382577,7.80127,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,2.06113,0.680988,0.87256,2.09294,0.577088,0.363423,1.00998,3.25206,1.15522,0.312599,5.61831,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,1.45393|tfbs_overrepresentation_jaspar=MA0003.1;2.72292,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;2.50943,MA0009.1;1.11255,MA0014.1;2.48957,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;1.08193,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;4.86963,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;2.08296,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;2.58868,MA0089.1;0,MA0090.1;1.36977,MA0091.1;1.52322,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.973423,MA0115.1;1.35895,MA0116.1;1.76306,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;2.01656,MA0146.1;4.16116,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;5.20522,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.880827,MA0150.1;2.32613,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.72541,MA0163.1;0.680296,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;9.98501,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1960_Mesenchymal_Smooth_cholangiocellular_hepatic_bile_Fibroblast_mesenchymal
|id=C1960
}}

Latest revision as of 11:55, 17 September 2013


Full id: C1960_Mesenchymal_Smooth_cholangiocellular_hepatic_bile_Fibroblast_mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:33892081..33892101,-p1@ADAMTS12
Hg19::chr5:33892102..33892117,-p3@ADAMTS12
Hg19::chr5:33892118..33892144,-p2@ADAMTS12
Hg19::chr5:33892167..33892190,-p4@ADAMTS12
Hg19::chr5:33892204..33892218,-p6@ADAMTS12


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
somite1.05e-2371
presomitic mesoderm1.05e-2371
presumptive segmental plate1.05e-2371
dermomyotome1.05e-2371
trunk paraxial mesoderm1.05e-2371
dense mesenchyme tissue1.83e-2373
skeletal muscle tissue4.14e-2362
striated muscle tissue4.14e-2362
myotome4.14e-2362
paraxial mesoderm5.82e-2372
presumptive paraxial mesoderm5.82e-2372
muscle tissue7.86e-2364
musculature7.86e-2364
musculature of body7.86e-2364
epithelial vesicle9.57e-2278
trunk mesenchyme1.94e-19122
multilaminar epithelium2.71e-1983
mesenchyme1.03e-15160
entire embryonic mesenchyme1.03e-15160
organism subdivision1.85e-14264
unilaminar epithelium3.15e-14148
splanchnic layer of lateral plate mesoderm1.14e-1383
trunk7.14e-13199
vasculature5.67e-1278
vascular system5.67e-1278
cardiovascular system1.06e-10109
artery1.96e-1042
arterial blood vessel1.96e-1042
arterial system1.96e-1042
epithelial tube2.69e-10117
circulatory system4.63e-10112
cell layer7.02e-10309
systemic artery1.08e-0933
systemic arterial system1.08e-0933
multi-tissue structure2.69e-09342
epithelium3.05e-09306
epithelial tube open at both ends1.23e-0859
blood vessel1.23e-0859
blood vasculature1.23e-0859
vascular cord1.23e-0859
primordium4.89e-08160
smooth muscle tissue6.69e-0815
heart1.81e-0724
primitive heart tube1.81e-0724
primary heart field1.81e-0724
anterior lateral plate mesoderm1.81e-0724
heart tube1.81e-0724
heart primordium1.81e-0724
cardiac mesoderm1.81e-0724
cardiogenic plate1.81e-0724
heart rudiment1.81e-0724
vasculature of organ2.36e-0711
vessel2.59e-0768
blood vessel smooth muscle5.30e-0710
arterial system smooth muscle5.30e-0710
artery smooth muscle tissue5.30e-0710
aorta smooth muscle tissue5.30e-0710
Disease
Ontology termp-valuen
ovarian cancer8.21e-0814


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)
MA0003.12.72292
MA0004.10.626788
MA0006.10.452993
MA0007.12.50943
MA0009.11.11255
MA0014.12.48957
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.14.86963
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.08296
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.12.58868
MA0089.10
MA0090.11.36977
MA0091.11.52322
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.11.76306
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.12.01656
MA0146.14.16116
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.25.20522
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.12.32613
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.29.98501
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
EGR1#195854.988179094810140.0003237398000590710.00331059051976592



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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