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Coexpression cluster:C655: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.208137,0.329487,0.202418,0.320418,0.981802,0.319017,0.385011,0.303088,0.621506,0.0427817,0.293498,0.423573,0.0649383,0.37489,0.506988,0.549464,0.587543,0.412009,1.36919,0.246002,0.585797,0.511864,0.312425,0.167123,0.238419,0.443987,0.20034,0.310589,0.173154,0.399779,0.275306,0.622056,0.721119,0.234859,0.145955,0.305397,0.143715,0.320003,0.127608,0.570628,0.874039,0.261903,0.859837,0.973137,0.0138934,0.226447,0.385972,0.284438,0.803087,0.173249,0.456831,0.396393,0.126438,0.694739,0.841347,0.377467,0.176395,0.348876,0.177537,0.348003,0.660716,0.388062,0.0892869,0.561703,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.251183,0.312497,0.0300688,0.839414,0.224555,0.205774,0.733065,0.546008,0.609242,0.233499,0.074278,0.560705,0.403653,0.636937,0.789807,0.00329133,0.0226931,1.50483,0.480498,1.38705,1.01818,0.763867,2.60974,0.368116,0.171417,0.123575,0.248364,0.67819,0.484706,0.345246,0.803034,0.632556,0.672898,0.590971,0.519171,0.289709,0.576179,0.971972,0.238217,0.15924,0.211112,0.670274,0.198172,0.301413,0.971251,0.439271,0.0270384,0.753394,0.527634,0.750778,0.831412,0.478284,1.5335,0.413695,1.0796,0.546713,0.988587,0.642598,0.872646,0.124214,0.76453,0.277675,0.886589,0.410725,1.03079,0.0417786,0.744364,0.311068,0.989273,1.83943,1.43902,2.18994,0.38094,0.674844,0.52079,0.341558,0.505455,1.68078,0.259186,0.112739,0.0262543,0.0123511,0.764896,0.0843101,0.387634,1.15881,0.465765,2.15003,0.238466,0.21563,0.951654,0.747146,0.608503,0.21815,0.535644,0.402951,0.341994,0.383837,0.0203729
|tfbs_overrepresentation_jaspar=MA0003.1;0.00501742,MA0004.1;0.297884,MA0006.1;0.169524,MA0007.1;0.282081,MA0009.1;0.724811,MA0014.1;0.00634684,MA0017.1;0.199401,MA0019.1;0.428118,MA0024.1;0.6245,MA0025.1;0.854131,MA0027.1;2.32165,MA0028.1;0.181601,MA0029.1;0.642879,MA0030.1;0.63197,MA0031.1;0.570886,MA0038.1;0.387473,MA0040.1;0.648455,MA0041.1;0.313738,MA0042.1;0.286538,MA0043.1;0.725115,MA0046.1;0.714324,MA0048.1;0.30948,MA0050.1;0.287284,MA0051.1;0.997995,MA0052.1;0.652145,MA0055.1;0.0277818,MA0056.1;0,MA0057.1;0.294933,MA0058.1;0.219229,MA0059.1;0.218203,MA0060.1;0.2996,MA0061.1;0.255087,MA0063.1;0,MA0066.1;0.387854,MA0067.1;1.03434,MA0068.1;0.434546,MA0069.1;0.710614,MA0070.1;0.69985,MA0071.1;0.930644,MA0072.1;0.695528,MA0073.1;0.000945528,MA0074.1;0.383033,MA0076.1;0.231962,MA0077.1;0.688123,MA0078.1;0.473657,MA0081.1;0.623454,MA0083.1;0.732051,MA0084.1;1.21913,MA0087.1;0.693179,MA0088.1;0.0644248,MA0089.1;0,MA0090.1;0.682802,MA0091.1;0.30011,MA0092.1;0.268302,MA0093.1;0.171791,MA0095.1;0,MA0098.1;0,MA0100.1;0.399896,MA0101.1;0.517741,MA0103.1;0.489275,MA0105.1;0.10818,MA0106.1;1.0872,MA0107.1;0.385539,MA0108.2;1.39378,MA0109.1;0,MA0111.1;1.30787,MA0113.1;0.439505,MA0114.1;0.376635,MA0115.1;0.959312,MA0116.1;0.123927,MA0117.1;0.76111,MA0119.1;0.205526,MA0122.1;0.786181,MA0124.1;0.918678,MA0125.1;0.83671,MA0130.1;0,MA0131.1;0.490408,MA0132.1;0,MA0133.1;0,MA0135.1;1.7821,MA0136.1;0.393782,MA0139.1;0.0663461,MA0140.1;0.350813,MA0141.1;0.216821,MA0142.1;0.541045,MA0143.1;2.91707,MA0144.1;0.35188,MA0145.1;0.0753792,MA0146.1;0.191696,MA0147.1;0.126316,MA0148.1;0.319209,MA0149.1;0.90664,MA0062.2;0.0702147,MA0035.2;0.924091,MA0039.2;0.0190349,MA0138.2;0.474787,MA0002.2;0.280231,MA0137.2;0.186529,MA0104.2;0.088751,MA0047.2;0.413608,MA0112.2;0.0689988,MA0065.2;0.200291,MA0150.1;0.238884,MA0151.1;0,MA0152.1;0.356591,MA0153.1;0.820317,MA0154.1;0.105196,MA0155.1;0.167839,MA0156.1;0.18827,MA0157.1;0.515488,MA0158.1;0,MA0159.1;0.795271,MA0160.1;0.332385,MA0161.1;0,MA0162.1;0.00205586,MA0163.1;0.00707238,MA0164.1;0.450848,MA0080.2;0.171855,MA0018.2;0.425847,MA0099.2;0.356906,MA0079.2;0.00203337,MA0102.2;1.25596,MA0258.1;0.102521,MA0259.1;0.132107,MA0442.1;0
}}
}}

Revision as of 19:20, 22 January 2013


Full id: C655_mesothelioma_Mesothelial_hepatoma_cholangiocellular_Urothelial_glioma_serous



Phase1 CAGE Peaks

Hg19::chr11:5367168..5367185,-p@chr11:5367168..5367185
-
Hg19::chr11:79784329..79784335,-p@chr11:79784329..79784335
-
Hg19::chr1:87980155..87980198,+p@chr1:87980155..87980198
+
Hg19::chr2:233195304..233195346,+p@chr2:233195304..233195346
+
Hg19::chr2:234451186..234451205,-p5@USP40
Hg19::chr2:234733119..234733132,+p@chr2:234733119..234733132
+
Hg19::chr4:125341461..125341462,-p@chr4:125341461..125341462
-
Hg19::chr4:125341479..125341498,-p@chr4:125341479..125341498
-
Hg19::chr4:125341514..125341526,-p@chr4:125341514..125341526
-
Hg19::chr4:73761277..73761307,-p@chr4:73761277..73761307
-
Hg19::chr6:53761287..53761314,+p@chr6:53761287..53761314
+
Hg19::chr7:6285086..6285095,+p@chr7:6285086..6285095
+
Hg19::chr9:126131131..126131159,+p3@CRB2


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>

Cell Type
Ontology termp-valuen
mesothelial cell3.17e-5219
cortical cell of adrenal gland4.66e-212
lining cell1.12e-1758
barrier cell1.12e-1758
squamous epithelial cell2.47e-1663
steroid hormone secreting cell1.60e-143
mesodermal cell8.28e-09121
Uber Anatomy
Ontology termp-valuen
adrenal gland1.60e-143
adrenal cortex1.60e-143
adrenal/interrenal gland1.60e-143
Disease
Ontology termp-valuen
endocrine gland cancer6.34e-086


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)
MA0003.10.00501742
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.00634684
MA0017.10.199401
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.30948
MA0050.10.287284
MA0051.10.997995
MA0052.10.652145
MA0055.10.0277818
MA0056.10
MA0057.10.294933
MA0058.10.219229
MA0059.10.218203
MA0060.10.2996
MA0061.10.255087
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.434546
MA0069.10.710614
MA0070.10.69985
MA0071.10.930644
MA0072.10.695528
MA0073.10.000945528
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.623454
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.0644248
MA0089.10
MA0090.10.682802
MA0091.10.30011
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.517741
MA0103.10.489275
MA0105.10.10818
MA0106.11.0872
MA0107.10.385539
MA0108.21.39378
MA0109.10
MA0111.11.30787
MA0113.10.439505
MA0114.10.376635
MA0115.10.959312
MA0116.10.123927
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.11.7821
MA0136.10.393782
MA0139.10.0663461
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.12.91707
MA0144.10.35188
MA0145.10.0753792
MA0146.10.191696
MA0147.10.126316
MA0148.10.319209
MA0149.10.90664
MA0062.20.0702147
MA0035.20.924091
MA0039.20.0190349
MA0138.20.474787
MA0002.20.280231
MA0137.20.186529
MA0104.20.088751
MA0047.20.413608
MA0112.20.0689988
MA0065.20.200291
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.105196
MA0155.10.167839
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.795271
MA0160.10.332385
MA0161.10
MA0162.10.00205586
MA0163.10.00707238
MA0164.10.450848
MA0080.20.171855
MA0018.20.425847
MA0099.20.356906
MA0079.20.00203337
MA0102.21.25596
MA0258.10.102521
MA0259.10.132107
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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