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{{Coexpression_clusters
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.208834,0.32256,0.377566,0.342366,0.109684,0.322704,0.403482,0.181288,0.00247802,0.352328,7.09281e-07,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.0550411,0.512825,0.244656,0.192188,0.158985,0.174153,0.00489362,0.333309,0.249919,0.339517,0.0516568,0.198326,0.394084,0.458518,0.00476409,0.252005,0.0140681,0.238377,0.334983,0.197875,0.0461189,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.321404,0.225079,0.300542,0.083451,0.185715,0.345505,0.375521,0.271405,0.311201,0.0266853,0.306427,0.367733,0.0333601,0.208775,0.0886961,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.0083772,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.0478203,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.00268881,0.109077,0.144842,0.0604892,0.0248943,0.316879,0.116796,0.430541,0.00605341,0.224871,0.398887,0.0138446,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.110045,0.362154,0.480785,0.185476,0.00847033,0.344469,0.184651,0.303359,0.297596,0.018596,0.425912,0.0840133,0.259046,0.00922992,0.151046,0.483953,0.0687784,0.321735,0.15463,0.13907,0.00410146,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.0668707,0.27567,0.248127,0.33299,0.0858973,0.319112,0.172492|tfbs_overrepresentation_for_novel_motifs=1.26722,1.20042,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.859849,0.345702,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.94379,0.27659,0.417272,9.72002,1.06371,0.654459,1.00769,3.12855,0.415749,0.580638,0.132849,0.451846,0.476793,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.66643,1.23387,0.269111,1.30959,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.251545,0.166306,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,4.06216,0.381528,1.42387,1.06255,0.849074,1.14173,2.68381,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,0.596731,2.07682,0.370186,1.22546,0.841768,0.650322,1.80913,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572|tfbs_overrepresentation_jaspar=MA0003.1;0.136928,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.369468,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;1.18667,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;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;2.06887,MA0056.1;0,MA0057.1;0.189508,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;2.7757,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;22.1102,MA0074.1;0.730989,MA0076.1;2.29573,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;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,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;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;1.25946,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;0.143698,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.801354,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.469165,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;4.3662,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1682_schwannoma_Fibroblast_hepatoblastoma_Wilms_adrenal_Aortic_meningioma
|id=C1682
}}

Latest revision as of 11:50, 17 September 2013


Full id: C1682_schwannoma_Fibroblast_hepatoblastoma_Wilms_adrenal_Aortic_meningioma



Phase1 CAGE Peaks

Hg19::chr12:66218836..66218888,+p1@HMGA2
Hg19::chr12:66218904..66218913,+p11@HMGA2
Hg19::chr12:66218923..66218934,+p14@HMGA2
Hg19::chr12:66357214..66357233,+p13@HMGA2
Hg19::chr12:66358080..66358094,+p15@HMGA2


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
multilaminar epithelium3.75e-2383
somite1.98e-2071
presomitic mesoderm1.98e-2071
presumptive segmental plate1.98e-2071
dermomyotome1.98e-2071
trunk paraxial mesoderm1.98e-2071
dense mesenchyme tissue2.94e-2073
epithelial vesicle8.93e-2078
paraxial mesoderm9.26e-2072
presumptive paraxial mesoderm9.26e-2072
skeletal muscle tissue1.32e-1962
striated muscle tissue1.32e-1962
myotome1.32e-1962
unilaminar epithelium3.74e-19148
muscle tissue3.29e-1864
musculature3.29e-1864
musculature of body3.29e-1864
artery1.18e-1642
arterial blood vessel1.18e-1642
arterial system1.18e-1642
vasculature3.53e-1678
vascular system3.53e-1678
organism subdivision3.09e-15264
mesenchyme1.04e-14160
entire embryonic mesenchyme1.04e-14160
trunk mesenchyme4.38e-14122
epithelial tube4.70e-14117
epithelial tube open at both ends1.05e-1359
blood vessel1.05e-1359
blood vasculature1.05e-1359
vascular cord1.05e-1359
systemic artery2.32e-1333
systemic arterial system2.32e-1333
cell layer1.64e-12309
vessel2.29e-1268
epithelium5.30e-12306
splanchnic layer of lateral plate mesoderm7.65e-1283
cardiovascular system3.18e-11109
circulatory system2.99e-10112
trunk1.05e-09199
surface structure2.69e-0999
aorta1.20e-0821
aortic system1.20e-0821
head1.65e-0856
multi-tissue structure3.00e-08342
blood vessel smooth muscle5.00e-0810
arterial system smooth muscle5.00e-0810
artery smooth muscle tissue5.00e-0810
aorta smooth muscle tissue5.00e-0810
subdivision of head5.37e-0849
anatomical system1.47e-07624
anatomical group2.02e-07625
multi-cellular organism3.59e-07656
embryo4.91e-07592
anterior region of body8.85e-0762
craniocervical region8.85e-0762


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)
MA0003.10.136928
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.11.18667
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.12.06887
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.12.7757
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.122.1102
MA0074.10.730989
MA0076.12.29573
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
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
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.11.25946
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
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.24.3662
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
CTCF#1066444.288205098460020.005152015588243280.0239249157857065
JUNB#3726318.36637959589270.0003316319811700890.00337773673507148
TCF7L2#693436.462105937882410.006930108755689190.0293156315904015
TFAP2C#702236.485537165916130.006858951517940.029055813968611
ZZZ3#260093143.647927461147.21371177912933e-073.21550509816683e-05



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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