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Coexpression cluster:C231: Difference between revisions

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{{Coexpression_clusters
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,0.0244656,0.43842,0.0475379,1.43253,0.0374921,0.414397,0.0966708,0.0182977,0.015745,0.733315,0.0460563,0.0345569,0.36128,0.140411,0.122496,0.978331,0.0272041,0.379567,0.0753235,0.0572237,0.0862994,0.207991,0.0402277,0.0571966,0.511811,0.0849417,0.0493271,0.0419945,0.0609363,0.14148,0.257308,0.0918039,0.0012118,0.14844,0.00113983,0.0920149,0.336532,0.0138929,0.267853,0.0528835,0.0840192,0.356919,0.0651867,0.215107,0.148957,0.175423,0.468711,0.0494024,0.062065,0.159064,0.0561057,0.185058,0.285549,0.0352918,0.825844,0.11539,0.554891,0.114647,0.164079,0.150961,0.0973898,0.109063,0.0433443,0.311119,0.350587,0.658583,0.422519,0.516982,0.00923855,0.812951,0.000125992,0.28413,0.00686885,0.032065,0.773702,0.679771,0.134296,1.60122,0.299524,0.108558,1.04353,0.426899,0.248516,4.45207e-05,0.00633097,0.276879,0.534501,0.748573,0.423767,0.230543,0.897689,0.277969,0.0143876,0.47563,0.730334,0.174731,0.0733195,0.0248672,0.708606,0.147482,0.171477,0.124329,0.0884977,0.0702504,0.116504,0.580323,0.00766285,0.0112805,0.779162,0.169873,0.978733,0.200597,0.385616,0.147799,0.00512232,0.0125294,0.30836,0.173635,0.27828,0.529765,0.224371,0.397442,2.07804,0.101591,0.602081,0.153318,0.308831,0.108185,0.65322,0.330226,0.855401,1.51773,0.434176,0.00182522,0.31276,0.677953,0.400154,1.17966,0.796831,0.370915,0.335164,0.989142,0.089244,0.794504,0.992042,1.02612,0.286666,0.0861996,0.0204391,4.01707e-07,0.231247,0.0855301,0.347598,0.543107,0.503225,0.191428,0.420836,0.00535347,0.967808,0.219209,2.60793,0.0308107,0.318633,1.04064,0.0725803,0.962563,0.00240275|tfbs_overrepresentation_jaspar=MA0003.1;5.56899e-14,MA0004.1;0.0758368,MA0006.1;0.0138739,MA0007.1;0.013777,MA0009.1;1.75023,MA0014.1;3.3504e-09,MA0017.1;0.072348,MA0019.1;0.425954,MA0024.1;0.142868,MA0025.1;0.800437,MA0027.1;1.65408,MA0028.1;0.00282582,MA0029.1;2.09406,MA0030.1;0.147145,MA0031.1;0.737299,MA0038.1;0.625513,MA0040.1;1.47816,MA0041.1;0.21972,MA0042.1;0.178462,MA0043.1;0.204593,MA0046.1;0.197569,MA0048.1;0.00016639,MA0050.1;0.590231,MA0051.1;0.146796,MA0052.1;0.158952,MA0055.1;0.00267116,MA0056.1;0,MA0057.1;0.0903482,MA0058.1;0.0312766,MA0059.1;0.00558968,MA0060.1;0.00143531,MA0061.1;0.114122,MA0063.1;0,MA0066.1;0.626627,MA0067.1;0.43712,MA0068.1;0.0558467,MA0069.1;0.195175,MA0070.1;0.551797,MA0071.1;0.52739,MA0072.1;0.185556,MA0073.1;0.00857405,MA0074.1;0.612568,MA0076.1;0.00696909,MA0077.1;3.06124,MA0078.1;1.85726,MA0081.1;0.0916767,MA0083.1;0.209155,MA0084.1;0.596203,MA0087.1;0.541602,MA0088.1;0.123806,MA0089.1;0,MA0090.1;3.06921,MA0091.1;0.385792,MA0092.1;0.307878,MA0093.1;0.0144903,MA0095.1;0,MA0098.1;0,MA0100.1;0.0420486,MA0101.1;0.378628,MA0103.1;0.0413974,MA0105.1;0.0190537,MA0106.1;0.0502319,MA0107.1;0.8769,MA0108.2;0.361304,MA0109.1;0,MA0111.1;0.0488432,MA0113.1;0.0555453,MA0114.1;0.177951,MA0115.1;0.376065,MA0116.1;0.319273,MA0117.1;0.22866,MA0119.1;0.173567,MA0122.1;0.245976,MA0124.1;0.344064,MA0125.1;0.282149,MA0130.1;0,MA0131.1;0.0757356,MA0132.1;0,MA0133.1;0,MA0135.1;0.636585,MA0136.1;0.156505,MA0139.1;0.00236754,MA0140.1;0.830696,MA0141.1;0.0900529,MA0142.1;0.325628,MA0143.1;1.19377,MA0144.1;0.149521,MA0145.1;0.0447581,MA0146.1;0.000103846,MA0147.1;0.0196811,MA0148.1;0.228426,MA0149.1;0.0260116,MA0062.2;5.78111e-05,MA0035.2;1.63039,MA0039.2;0.00169129,MA0138.2;0.0692079,MA0002.2;0.145054,MA0137.2;0.260875,MA0104.2;0.00639385,MA0047.2;0.397271,MA0112.2;0.0601879,MA0065.2;0.080182,MA0150.1;0.241398,MA0151.1;0,MA0152.1;0.85347,MA0153.1;0.270235,MA0154.1;0.00316815,MA0155.1;0.00131199,MA0156.1;0.0620381,MA0157.1;1.02489,MA0158.1;0,MA0159.1;0.0198886,MA0160.1;0.470383,MA0161.1;0,MA0162.1;1.03902e-07,MA0163.1;8.63704e-06,MA0164.1;0.216326,MA0080.2;0.0483055,MA0018.2;0.0506682,MA0099.2;0.854714,MA0079.2;1.73915e-08,MA0102.2;0.629093,MA0258.1;0.348321,MA0259.1;0.0225426,MA0442.1;0}}
|full_id=C231_Mesothelial_mesenchymal_mesothelioma_Fibroblast_Preadipocyte_leiomyoma_mycosis
|id=C231
}}

Latest revision as of 11:01, 17 September 2013


Full id: C231_Mesothelial_mesenchymal_mesothelioma_Fibroblast_Preadipocyte_leiomyoma_mycosis



Phase1 CAGE Peaks

Hg19::chr10:29248821..29248844,-p@chr10:29248821..29248844
-
Hg19::chr10:29248873..29248901,-p@chr10:29248873..29248901
-
Hg19::chr11:111724419..111724469,-p@chr11:111724419..111724469
-
Hg19::chr11:111724532..111724542,-p@chr11:111724532..111724542
-
Hg19::chr11:111724543..111724555,-p@chr11:111724543..111724555
-
Hg19::chr11:127841493..127841504,-p@chr11:127841493..127841504
-
Hg19::chr11:127875726..127875731,-p@chr11:127875726..127875731
-
Hg19::chr12:120502376..120502385,+p8@CCDC64
Hg19::chr12:120502386..120502408,+p1@CCDC64
Hg19::chr13:108074395..108074398,-p@chr13:108074395..108074398
-
Hg19::chr13:38083829..38083838,+p@chr13:38083829..38083838
+
Hg19::chr13:38083855..38083873,+p@chr13:38083855..38083873
+
Hg19::chr13:38143481..38143491,-p@chr13:38143481..38143491
-
Hg19::chr13:38143907..38143931,+p@chr13:38143907..38143931
+
Hg19::chr13:38144712..38144754,+p@chr13:38144712..38144754
+
Hg19::chr14:45251913..45251924,-p2@ENST00000556405
Hg19::chr14:45251956..45251976,-p1@ENST00000556405
Hg19::chr14:45252031..45252036,-p5@ENST00000556405
Hg19::chr14:45252056..45252063,-p4@ENST00000556405
Hg19::chr14:45252105..45252117,-p3@ENST00000556405
Hg19::chr15:101445820..101445832,-p@chr15:101445820..101445832
-
Hg19::chr15:63449025..63449064,-p3@RPS27L
Hg19::chr15:63450169..63450189,-p5@RPS27L
Hg19::chr15:63450192..63450226,-p2@RPS27L
Hg19::chr15:63536192..63536195,+p@chr15:63536192..63536195
+
Hg19::chr17:38128375..38128405,+p@chr17:38128375..38128405
+
Hg19::chr17:67031950..67031959,-p5@ABCA9
Hg19::chr18:20419512..20419521,-p@chr18:20419512..20419521
-
Hg19::chr18:7813360..7813367,+p@chr18:7813360..7813367
+
Hg19::chr19:10687907..10687918,-p@chr19:10687907..10687918
-
Hg19::chr1:22745420..22745427,-p@chr1:22745420..22745427
-
Hg19::chr1:22745449..22745465,-p@chr1:22745449..22745465
-
Hg19::chr1:22745469..22745477,-p@chr1:22745469..22745477
-
Hg19::chr1:59522284..59522317,+p@chr1:59522284..59522317
+
Hg19::chr1:64686211..64686219,+p@chr1:64686211..64686219
+
Hg19::chr20:1435971..1435982,-p@chr20:1435971..1435982
-
Hg19::chr20:48184518..48184520,-p@chr20:48184518..48184520
-
Hg19::chr20:48184812..48184818,-p13@PTGIS
Hg19::chr22:37633537..37633546,-p@chr22:37633537..37633546
-
Hg19::chr2:135168644..135168657,+p@chr2:135168644..135168657
+
Hg19::chr2:135168804..135168814,+p@chr2:135168804..135168814
+
Hg19::chr2:151742292..151742317,+p@chr2:151742292..151742317
+
Hg19::chr2:220309507..220309512,+p33@SPEG
Hg19::chr2:25326312..25326322,+p@chr2:25326312..25326322
+
Hg19::chr3:8989081..8989115,-p@chr3:8989081..8989115
-
Hg19::chr4:142141683..142141694,+p3@ZNF330
Hg19::chr4:28801404..28801410,-p@chr4:28801404..28801410
-
Hg19::chr4:38119558..38119577,+p@chr4:38119558..38119577
+
Hg19::chr5:149682252..149682265,-p6@ARSI
Hg19::chr5:149682332..149682346,-p3@ARSI
Hg19::chr6:159309490..159309509,+p10@C6orf99
Hg19::chr7:43584118..43584127,-p@chr7:43584118..43584127
-
Hg19::chr8:117463964..117463997,-p@chr8:117463964..117463997
-
Hg19::chr8:125754675..125754679,-p@chr8:125754675..125754679
-
Hg19::chr8:74498501..74498510,-p@chr8:74498501..74498510
-
Hg19::chr9:113208581..113208593,-p@chr9:113208581..113208593
-
Hg19::chr9:118053068..118053087,+p1@DEC1
Hg19::chr9:16727001..16727016,+p@chr9:16727001..16727016
+
Hg19::chr9:33185050..33185064,-p@chr9:33185050..33185064
-
Hg19::chr9:33185073..33185094,-p@chr9:33185073..33185094
-
Hg19::chr9:35027511..35027519,-p@chr9:35027511..35027519
-


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:0008116prostaglandin-I synthase activity0.0280230778288002



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 cell2.31e-2419
lining cell2.47e-0858
barrier cell2.47e-0858
squamous epithelial cell1.05e-0763
Uber Anatomy
Ontology termp-valuen
right ovary6.77e-075
Disease
Ontology termp-valuen
ovarian cancer8.79e-1914
female reproductive organ cancer4.19e-1027
reproductive organ cancer1.87e-0929


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)
MA0003.15.56899e-14
MA0004.10.0758368
MA0006.10.0138739
MA0007.10.013777
MA0009.11.75023
MA0014.13.3504e-09
MA0017.10.072348
MA0019.10.425954
MA0024.10.142868
MA0025.10.800437
MA0027.11.65408
MA0028.10.00282582
MA0029.12.09406
MA0030.10.147145
MA0031.10.737299
MA0038.10.625513
MA0040.11.47816
MA0041.10.21972
MA0042.10.178462
MA0043.10.204593
MA0046.10.197569
MA0048.10.00016639
MA0050.10.590231
MA0051.10.146796
MA0052.10.158952
MA0055.10.00267116
MA0056.10
MA0057.10.0903482
MA0058.10.0312766
MA0059.10.00558968
MA0060.10.00143531
MA0061.10.114122
MA0063.10
MA0066.10.626627
MA0067.10.43712
MA0068.10.0558467
MA0069.10.195175
MA0070.10.551797
MA0071.10.52739
MA0072.10.185556
MA0073.10.00857405
MA0074.10.612568
MA0076.10.00696909
MA0077.13.06124
MA0078.11.85726
MA0081.10.0916767
MA0083.10.209155
MA0084.10.596203
MA0087.10.541602
MA0088.10.123806
MA0089.10
MA0090.13.06921
MA0091.10.385792
MA0092.10.307878
MA0093.10.0144903
MA0095.10
MA0098.10
MA0100.10.0420486
MA0101.10.378628
MA0103.10.0413974
MA0105.10.0190537
MA0106.10.0502319
MA0107.10.8769
MA0108.20.361304
MA0109.10
MA0111.10.0488432
MA0113.10.0555453
MA0114.10.177951
MA0115.10.376065
MA0116.10.319273
MA0117.10.22866
MA0119.10.173567
MA0122.10.245976
MA0124.10.344064
MA0125.10.282149
MA0130.10
MA0131.10.0757356
MA0132.10
MA0133.10
MA0135.10.636585
MA0136.10.156505
MA0139.10.00236754
MA0140.10.830696
MA0141.10.0900529
MA0142.10.325628
MA0143.11.19377
MA0144.10.149521
MA0145.10.0447581
MA0146.10.000103846
MA0147.10.0196811
MA0148.10.228426
MA0149.10.0260116
MA0062.25.78111e-05
MA0035.21.63039
MA0039.20.00169129
MA0138.20.0692079
MA0002.20.145054
MA0137.20.260875
MA0104.20.00639385
MA0047.20.397271
MA0112.20.0601879
MA0065.20.080182
MA0150.10.241398
MA0151.10
MA0152.10.85347
MA0153.10.270235
MA0154.10.00316815
MA0155.10.00131199
MA0156.10.0620381
MA0157.11.02489
MA0158.10
MA0159.10.0198886
MA0160.10.470383
MA0161.10
MA0162.11.03902e-07
MA0163.18.63704e-06
MA0164.10.216326
MA0080.20.0483055
MA0018.20.0506682
MA0099.20.854714
MA0079.21.73915e-08
MA0102.20.629093
MA0258.10.348321
MA0259.10.0225426
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

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