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Coexpression cluster:C341: Difference between revisions

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{{Coexpression_clusters
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746,0.97434,0.957737,0.861764,0.767774,0.660659,0.987302,0.771379,0.922868,0.670003,0.62779,0.603059,0.874061,0.85085,0.459273,0.555776,0.861006,0.690085,0.763601,0.880991,0.561184,0.930932,0.220383,0.920878,0.725564|tfbs_overrepresentation_for_novel_motifs=0.0391464,0.00254248,0.146286,1.06548,0.495643,0.634731,0.13057,0.0995429,0.208201,0.000202207,0.0780977,0.155358,0.017752,0.392606,2.55059,0.303553,0.274123,0.0147216,0.00365927,0.648082,0.339391,0.0444592,0.0881331,0.105169,0.192249,0.169033,0.518265,0.293913,0.111883,1.15562,0.520703,0.301321,0.479525,0.136379,0.0183975,3.0954e-05,0.0177865,0.0922784,0.171279,0.0259523,0.401415,0.062417,0.412896,0.783873,0.322092,0.0465565,0.131171,0.2558,1.08348,0.270954,0.177819,0.137739,0.0423185,0.360536,0.486376,0.125892,0.516012,0.108703,0.0815711,0.108193,0.332512,0.132479,0.851117,0.254197,0.142578,0.651245,0.562972,0.901485,0.293563,0.749341,0.0574197,0.894411,0.00357758,0.48467,0.00266031,0.35094,0.681879,0.679569,4.98706,1.12226,1.30036,0.705404,0.862965,0.607891,1.12338,1.78248e-06,0.00194292,0.0299496,0.19436,0.996295,0.646289,0.418934,0.314004,0.503644,0.0260292,0.829334,0.455633,0.346841,0.197346,0.123091,0.0657404,0.833695,0.342487,0.276796,0.222295,0.0761449,0.265312,3.19942,0.191981,0.0222238,0.0403126,0.340332,0.329154,0.0822381,0.603172,0.392926,0.00482095,0.518154,0.647486,0.0112259,0.477624,0.562637,0.628534,0.455006,0.703324,0.242821,0.399788,0.317804,0.514129,1.16897,0.419503,0.0700713,0.526577,1.41918,0.657947,0.0264802,0.87165,0.0873984,0.619678,1.43971,1.0467,0.586378,0.128038,0.344087,0.223488,0.104448,0.212265,1.2832,0.0611342,0.287878,0.0734517,4.98319e-05,2.82524,0.0297034,0.132211,1.83091,0.184011,0.242525,0.0517159,0.042112,0.585299,0.404642,0.290564,0.0431301,0.234512,2.00234,0.126256,0.406823,3.09231e-05|tfbs_overrepresentation_jaspar=MA0003.1;1.54157e-10,MA0004.1;0.275233,MA0006.1;0.490695,MA0007.1;0.252431,MA0009.1;0.385713,MA0014.1;8.76096e-06,MA0017.1;0.142607,MA0019.1;0.158371,MA0024.1;0.303271,MA0025.1;1.2445,MA0027.1;1.91867,MA0028.1;0.0294248,MA0029.1;0.318031,MA0030.1;0.30925,MA0031.1;0.723388,MA0038.1;0.13211,MA0040.1;0.322542,MA0041.1;0.298588,MA0042.1;1.39887,MA0043.1;0.38597,MA0046.1;0.376892,MA0048.1;0.00417477,MA0050.1;0.074905,MA0051.1;0.129756,MA0052.1;0.325534,MA0055.1;1.62186,MA0056.1;0,MA0057.1;0.16673,MA0058.1;0.379924,MA0059.1;0.377421,MA0060.1;0.850458,MA0061.1;0.070207,MA0063.1;0,MA0066.1;0.132349,MA0067.1;0.661236,MA0068.1;0.00178979,MA0069.1;0.373781,MA0070.1;2.56598,MA0071.1;0.111216,MA0072.1;0.361192,MA0073.1;1.02142e-06,MA0074.1;0.129338,MA0076.1;0.0488952,MA0077.1;0.355047,MA0078.1;0.189533,MA0081.1;0.672921,MA0083.1;0.391829,MA0084.1;0.834984,MA0087.1;0.359239,MA0088.1;0.0271964,MA0089.1;0,MA0090.1;0.199262,MA0091.1;3.30578,MA0092.1;1.30387,MA0093.1;0.26762,MA0095.1;0,MA0098.1;0,MA0100.1;0.13997,MA0101.1;0.0269576,MA0103.1;1.50562,MA0105.1;0.0106284,MA0106.1;0.156032,MA0107.1;0.0122904,MA0108.2;0.259018,MA0109.1;0,MA0111.1;0.0590735,MA0113.1;0.497497,MA0114.1;2.36085,MA0115.1;0.592273,MA0116.1;0.0615009,MA0117.1;1.06978,MA0119.1;0.976089,MA0122.1;0.438159,MA0124.1;0.555413,MA0125.1;1.21157,MA0130.1;0,MA0131.1;0.201414,MA0132.1;0,MA0133.1;0,MA0135.1;0.410584,MA0136.1;0.136083,MA0139.1;0.00305399,MA0140.1;0.10984,MA0141.1;0.374053,MA0142.1;0.238557,MA0143.1;0.166108,MA0144.1;0.133428,MA0145.1;0.00452149,MA0146.1;2.23771e-05,MA0147.1;0.168618,MA0148.1;1.56876,MA0149.1;0.104897,MA0062.2;0.148751,MA0035.2;0.109476,MA0039.2;0.000512967,MA0138.2;4.87984,MA0002.2;0.186201,MA0137.2;0.127245,MA0104.2;0.0964482,MA0047.2;1.43053,MA0112.2;0.0121201,MA0065.2;0.14488,MA0150.1;0.0518993,MA0151.1;0,MA0152.1;0.113254,MA0153.1;0.467885,MA0154.1;0.00995799,MA0155.1;0.0100866,MA0156.1;0.129291,MA0157.1;0.626418,MA0158.1;0,MA0159.1;0.0640962,MA0160.1;0.0992022,MA0161.1;0,MA0162.1;7.90637e-06,MA0163.1;1.15799e-05,MA0164.1;0.173709,MA0080.2;0.499271,MA0018.2;0.156863,MA0099.2;1.76427,MA0079.2;1.25675e-06,MA0102.2;0.870137,MA0258.1;0.0431952,MA0259.1;0.014781,MA0442.1;0}}
|full_id=C341_giant_large_Fibroblast_Mesenchymal_Alveolar_Mesothelial_mesothelioma
|id=C341
}}

Latest revision as of 11:20, 17 September 2013


Full id: C341_giant_large_Fibroblast_Mesenchymal_Alveolar_Mesothelial_mesothelioma



Phase1 CAGE Peaks

Hg19::chr10:4828673..4828695,+p10@AKR1E2
Hg19::chr10:4828763..4828786,+p7@AKR1E2
Hg19::chr10:4828815..4828822,+p11@AKR1E2
Hg19::chr10:4828859..4828883,+p6@AKR1E2
Hg19::chr10:4832416..4832424,-p@chr10:4832416..4832424
-
Hg19::chr11:28723970..28723983,+p3@ENST00000513853
Hg19::chr11:28724030..28724037,+p6@ENST00000513853
Hg19::chr12:120662266..120662274,-p65@PXN
Hg19::chr12:120662499..120662559,-p3@PXN
Hg19::chr12:120662701..120662711,-p58@PXN
Hg19::chr12:120662730..120662751,-p46@PXN
Hg19::chr12:26126668..26126674,+p27@RASSF8
Hg19::chr12:26126681..26126692,+p8@RASSF8
Hg19::chr12:66035928..66035945,-p1@ENST00000535315
p1@ENST00000537298
Hg19::chr12:66035968..66035976,-p1@ENST00000537250
Hg19::chr12:66035982..66035985,-p3@ENST00000537250
Hg19::chr12:66035988..66035995,-p2@ENST00000537250
Hg19::chr12:66036060..66036071,-p4@ENST00000539653
Hg19::chr12:66036083..66036098,-p3@ENST00000539653
Hg19::chr12:66036125..66036136,-p2@ENST00000539653
Hg19::chr12:66036137..66036157,-p1@ENST00000539653
p2@ENST00000544557
Hg19::chr12:66036191..66036200,-p3@ENST00000544557
Hg19::chr12:66036219..66036262,-p1@ENST00000544557
Hg19::chr15:33384526..33384543,-p@chr15:33384526..33384543
-
Hg19::chr15:33384561..33384569,-p@chr15:33384561..33384569
-
Hg19::chr1:172902742..172902768,-p@chr1:172902742..172902768
-
Hg19::chr2:239344630..239344631,+p20@ASB1
Hg19::chr2:36805997..36806020,-p10@FEZ2
Hg19::chr2:36806173..36806191,-p14@FEZ2
Hg19::chr2:36806197..36806224,-p11@FEZ2
Hg19::chr2:36806228..36806237,-p24@FEZ2
Hg19::chr2:36806248..36806258,-p23@FEZ2
Hg19::chr5:14200357..14200390,+p@chr5:14200357..14200390
+


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:0007165signal transduction0.0175341130992519
GO:0017166vinculin binding0.0175341130992519
GO:0007154cell communication0.0175341130992519
GO:0051674localization of cell0.0175341130992519
GO:0006928cell motility0.0175341130992519
GO:0030539male genitalia development0.0206567778714676
GO:0048806genitalia development0.0236046189169336
GO:0042036negative regulation of cytokine biosynthetic process0.0244745405962095
GO:0007172signal complex assembly0.0244745405962095
GO:0046546development of primary male sexual characteristics0.0357782122939305
GO:0046661male sex differentiation0.0400209603080005
GO:0017148negative regulation of translation0.0469851050101578
GO:0031327negative regulation of cellular biosynthetic process0.047384859189351
GO:0009890negative regulation of biosynthetic process0.047384859189351
GO:0007411axon guidance0.047384859189351
GO:0045137development of primary sexual characteristics0.047384859189351
GO:0042035regulation of cytokine biosynthetic process0.047384859189351
GO:0042089cytokine biosynthetic process0.047384859189351
GO:0042107cytokine metabolic process0.047384859189351
GO:0043623cellular protein complex assembly0.047384859189351



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><br><br>disease_data<br>

Disease
Ontology termp-valuen
lung large cell carcinoma5.96e-343
non-small cell lung carcinoma5.15e-215
lung carcinoma2.45e-129
lung cancer5.93e-0815
respiratory system cancer1.54e-0716


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)
MA0003.11.54157e-10
MA0004.10.275233
MA0006.10.490695
MA0007.10.252431
MA0009.10.385713
MA0014.18.76096e-06
MA0017.10.142607
MA0019.10.158371
MA0024.10.303271
MA0025.11.2445
MA0027.11.91867
MA0028.10.0294248
MA0029.10.318031
MA0030.10.30925
MA0031.10.723388
MA0038.10.13211
MA0040.10.322542
MA0041.10.298588
MA0042.11.39887
MA0043.10.38597
MA0046.10.376892
MA0048.10.00417477
MA0050.10.074905
MA0051.10.129756
MA0052.10.325534
MA0055.11.62186
MA0056.10
MA0057.10.16673
MA0058.10.379924
MA0059.10.377421
MA0060.10.850458
MA0061.10.070207
MA0063.10
MA0066.10.132349
MA0067.10.661236
MA0068.10.00178979
MA0069.10.373781
MA0070.12.56598
MA0071.10.111216
MA0072.10.361192
MA0073.11.02142e-06
MA0074.10.129338
MA0076.10.0488952
MA0077.10.355047
MA0078.10.189533
MA0081.10.672921
MA0083.10.391829
MA0084.10.834984
MA0087.10.359239
MA0088.10.0271964
MA0089.10
MA0090.10.199262
MA0091.13.30578
MA0092.11.30387
MA0093.10.26762
MA0095.10
MA0098.10
MA0100.10.13997
MA0101.10.0269576
MA0103.11.50562
MA0105.10.0106284
MA0106.10.156032
MA0107.10.0122904
MA0108.20.259018
MA0109.10
MA0111.10.0590735
MA0113.10.497497
MA0114.12.36085
MA0115.10.592273
MA0116.10.0615009
MA0117.11.06978
MA0119.10.976089
MA0122.10.438159
MA0124.10.555413
MA0125.11.21157
MA0130.10
MA0131.10.201414
MA0132.10
MA0133.10
MA0135.10.410584
MA0136.10.136083
MA0139.10.00305399
MA0140.10.10984
MA0141.10.374053
MA0142.10.238557
MA0143.10.166108
MA0144.10.133428
MA0145.10.00452149
MA0146.12.23771e-05
MA0147.10.168618
MA0148.11.56876
MA0149.10.104897
MA0062.20.148751
MA0035.20.109476
MA0039.20.000512967
MA0138.24.87984
MA0002.20.186201
MA0137.20.127245
MA0104.20.0964482
MA0047.21.43053
MA0112.20.0121201
MA0065.20.14488
MA0150.10.0518993
MA0151.10
MA0152.10.113254
MA0153.10.467885
MA0154.10.00995799
MA0155.10.0100866
MA0156.10.129291
MA0157.10.626418
MA0158.10
MA0159.10.0640962
MA0160.10.0992022
MA0161.10
MA0162.17.90637e-06
MA0163.11.15799e-05
MA0164.10.173709
MA0080.20.499271
MA0018.20.156863
MA0099.21.76427
MA0079.21.25675e-06
MA0102.20.870137
MA0258.10.0431952
MA0259.10.014781
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
EP300#2033122.463251536808440.001814354306423650.0108983349288882
RAD21#5885123.765466871075033.32121315067201e-050.000660065043278848
STAT3#677482.550173332643450.01055091674989140.0389897103687606
TCF7L2#6934123.916427841140852.23995125295158e-050.000490025699428174



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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