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Coexpression cluster:C1885: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,1.25018,0.654974,0.454983,0.653236,1.73914,0.324142,0.859849,0.106358,0.621241,1.83296,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.167776,1.25032,0.384437,1.55551,0.44943,1.35492,0.802434,0.25115,1.55072,0.458349,0.233785,1.45697,1.00172,0.359091,0.758594,3.83647,0.195238,1.87167,1.57519,0.388123,0.301779,0.415749,1.42042,0.132849,0.451846,2.90891,1.32072,0.734485,1.48156,0.124583,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,1.72052,0.4631,0.689906,1.22844,1.64682,1.04369,0.736968,0.321912,0.935408,1.78554,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,2.36503,1.23387,1.36104,4.6455,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,6.14155,0.166306,0.647361,0.844289,1.79645,1.41984,1.15413,3.8027,0.367039,2.9911,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.95251,2.20213,2.39589,0.494368,0.631235,1.37132,0.412056,6.49685,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,1.18046,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,1.00998,4.02626,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0938701
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,1.25018,0.654974,0.454983,0.653236,1.73914,0.324142,0.859849,0.106358,0.621241,1.83296,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.167776,1.25032,0.384437,1.55551,0.44943,1.35492,0.802434,0.25115,1.55072,0.458349,0.233785,1.45697,1.00172,0.359091,0.758594,3.83647,0.195238,1.87167,1.57519,0.388123,0.301779,0.415749,1.42042,0.132849,0.451846,2.90891,1.32072,0.734485,1.48156,0.124583,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,1.72052,0.4631,0.689906,1.22844,1.64682,1.04369,0.736968,0.321912,0.935408,1.78554,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,2.36503,1.23387,1.36104,4.6455,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,6.14155,0.166306,0.647361,0.844289,1.79645,1.41984,1.15413,3.8027,0.367039,2.9911,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.95251,2.20213,2.39589,0.494368,0.631235,1.37132,0.412056,6.49685,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,1.18046,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,1.00998,4.02626,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0938701
|tfbs_overrepresentation_jaspar=MA0003.1;1.80249,MA0004.1;2.5741,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.161847,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;5.79033,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;1.05691,MA0058.1;3.29768,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.791444,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;4.00811,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.00220137,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;0.412364,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;4.06535,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;1.12656,MA0105.1;0.520776,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;0.382106,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;2.96863,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;1.39943,MA0146.1;0.333008,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.15493,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.839774,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;1.3196,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.382496,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;3.06493,MA0099.2;0.699641,MA0079.2;0.340387,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.02361,MA0442.1;0
}}
}}

Revision as of 20:15, 22 January 2013


Full id: C1885_neuroectodermal_nonsmall_small_neuroblastoma_embryonic_merkel_hairy



Phase1 CAGE Peaks

Hg19::chr2:176971685..176971700,+p6@HOXD11
Hg19::chr2:176971980..176971995,+p9@HOXD11
Hg19::chr2:176972000..176972025,+p4@HOXD11
Hg19::chr2:176972047..176972063,+p7@HOXD11
Hg19::chr2:176972082..176972096,+p8@HOXD11


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
urinary system structure3.06e-1647
renal system9.17e-1648
kidney2.44e-1426
kidney mesenchyme2.44e-1426
upper urinary tract2.44e-1426
kidney rudiment2.44e-1426
kidney field2.44e-1426
cavitated compound organ4.10e-1331
larynx1.55e-129
nephron tubule epithelium6.08e-1210
nephron epithelium6.89e-1215
renal tubule6.89e-1215
nephron tubule6.89e-1215
nephron6.89e-1215
uriniferous tubule6.89e-1215
nephrogenic mesenchyme6.89e-1215
excretory tube5.38e-1116
kidney epithelium5.38e-1116
cortex of kidney8.14e-1012
renal parenchyma8.14e-1012
cortex1.58e-0715
parenchyma1.58e-0715
Disease
Ontology termp-valuen
cell type cancer5.20e-15143
carcinoma1.60e-11106
disease of cellular proliferation1.81e-10239
neuroectodermal tumor5.11e-1010
cancer1.27e-09235
squamous cell carcinoma3.12e-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)
MA0003.11.80249
MA0004.12.5741
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
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
MA0043.15.79033
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.11.05691
MA0058.13.29768
MA0059.10.522232
MA0060.10.321781
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.14.00811
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.14.06535
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.12656
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
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
MA0139.12.96863
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.11.39943
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.3196
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.23.06493
MA0099.20.699641
MA0079.20.340387
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
ATF3#467417.9705396208071.89252338486495e-050.000429028108947059
CEBPB#105146.376918100659850.001113944176677320.0076569182485193
CTCF#1066455.360256373075030.0002259278299937090.00249980682664614
E2F1#186954.907389214879320.0003512818099256460.00353172130793459
SUZ12#23512550.11578091106293.15480790456198e-092.62537834856214e-07
USF1#739145.089199421766370.00266867775360040.0147218485056134
USF2#7392410.39375790805570.0001646179728687530.00202718269879021
ZNF263#1012758.221841637010682.6606316672286e-050.000571403887916282



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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