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Coexpression cluster:C483: Difference between revisions

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{{Coexpression_clusters
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328633,0.0398303,0.774903,0.265647,0.768597,0.278439,0.678373,0.608078,0.139297,0.500634,0.716164,0.372098,0.00519713,0.778083,0.916061,0.88906,1.30225e-06,0.435666,0.777951,0.528816,0.307401,0.308222,0.664564,0.418135,0.242076,0.308036,0.923489,0.867731,0.794586,0.749966,0.830331,0.000625364,0.431766,0.497647,0.357228,0.579675,0.355967,0.521255,0.367148,0.410674,0.600976,0.537305,0.259737,0.369972,0.465206,0.220875,0.61963,0.0687336,0.00285387,0.657991,0.158852,0.639009,3.63643e-08,0.860687,0.000161049,0.0309519,0.905799,0.309561,0.728566,0.891814,0.336109,0.610123,0.688882,0.78558,0.772657,0.895035,0.00255881,0.487017,0.559835,0.805978,0.81534,0.197172,4.9966e-11,0.16965,0.378903,0.891379,0.571197,0.698586,0.816014,0.480558,0.000430039,0.0940526,0.78836,0.489274,0.450622,1.47221e-05,0.357416,0.684379,0.0208572,0.388459,0.877982,0.508343,0.237038,1.04372e-11,0.107926,0.802061,0.000192316,0.454623,0.0330174|tfbs_overrepresentation_for_novel_motifs=0.111472,9.41696e-05,0.107302,1.09465,0.0849521,0.197892,0.253108,0.324098,0.0337392,0.00692657,0.177199,0.286323,0.0213511,0.244498,0.0842592,1.09318,0.43322,0.468601,0.481763,0.755249,0.707996,0.00152753,0.192508,0.0823774,0.134089,0.304148,0.0164598,0.191013,0.0865304,0.0631269,0.489389,0.465029,0.393386,0.0955518,0.0681935,3.55971,0.0667305,0.1987,0.206488,3.83139,0.0675531,0.152186,0.00209989,3.34004,0.0849878,0.394509,0.253928,0.169954,0.0016831,0.292421,0.315441,0.262847,0.108424,0.532773,0.671855,0.246686,0.620478,0.222594,0.0132181,0.221865,0.500944,0.255713,0.319823,0.409576,0.269358,0.380605,0.754286,1.10771,0.456006,0.950487,0.143869,0.336341,0.00682481,0.670004,0.020227,0.078586,0.0144775,0.395294,0.45319,0.130356,0.109737,0.408665,0.269087,0.0355014,0.622646,0.000236156,0.00447196,0.159385,0.336397,1.20481,1.96442,0.598,0.4797,1.111,0.0853298,0.0539379,0.024242,0.517267,0.340143,0.00964183,1.69347,0.474756,0.512318,0.436368,0.97011,0.174162,0.422802,0.241933,0.133935,0.0770225,0.364924,0.509866,0.104228,0.183573,0.797061,7.64274,0.000418211,0.161925,0.378653,2.67604,0.662347,0.334429,0.195973,1.39281,0.90249,0.395934,0.248345,0.484077,1.6739,0.054333,0.598629,0.164582,0.715286,2.12451,0.854902,0.0111458,0.158817,0.191402,0.814541,1.65405,1.25623,0.779227,0.249639,0.514137,0.372477,7.21912,0.35869,1.49614,0.150069,0.0473483,0.030735,0.00178079,0.598976,0.0312069,0.255347,0.980005,0.32333,0.0779979,0.134125,0.116987,0.77808,0.582159,0.452507,0.118854,0.385896,0.740042,0.0427574,0.702336,0.00090172|tfbs_overrepresentation_jaspar=MA0003.1;1.82551e-06,MA0004.1;0.180726,MA0006.1;0.0840255,MA0007.1;0.168078,MA0009.1;0.561062,MA0014.1;3.08855e-05,MA0017.1;0.105116,MA0019.1;1.43848,MA0024.1;0.467291,MA0025.1;0.684106,MA0027.1;2.13512,MA0028.1;0.0924235,MA0029.1;3.12101,MA0030.1;0.474212,MA0031.1;0.41796,MA0038.1;0.25521,MA0040.1;0.489524,MA0041.1;0.193578,MA0042.1;0.171628,MA0043.1;0.561349,MA0046.1;0.551181,MA0048.1;0.238801,MA0050.1;5.56259,MA0051.1;2.80282,MA0052.1;0.492957,MA0055.1;3.08726,MA0056.1;0,MA0057.1;0.00684412,MA0058.1;0.119655,MA0059.1;1.24352,MA0060.1;0.0338613,MA0061.1;0.0254296,MA0063.1;0,MA0066.1;0.255535,MA0067.1;0.858361,MA0068.1;0.614744,MA0069.1;0.547689,MA0070.1;0.537571,MA0071.1;0.22617,MA0072.1;0.533514,MA0073.1;6.97536e-08,MA0074.1;0.251422,MA0076.1;0.129195,MA0077.1;0.526569,MA0078.1;0.33032,MA0081.1;0.118989,MA0083.1;0.567893,MA0084.1;1.03923,MA0087.1;0.531309,MA0088.1;0.0132273,MA0089.1;0,MA0090.1;0.138104,MA0091.1;0.182521,MA0092.1;0.157193,MA0093.1;0.0855877,MA0095.1;0,MA0098.1;0,MA0100.1;0.734012,MA0101.1;0.0872967,MA0103.1;1.99485,MA0105.1;0.00533645,MA0106.1;0.28721,MA0107.1;0.0527035,MA0108.2;0.415325,MA0109.1;0,MA0111.1;0.146643,MA0113.1;0.300221,MA0114.1;0.0506063,MA0115.1;1.84688,MA0116.1;1.17696,MA0117.1;0.595385,MA0119.1;0.109564,MA0122.1;0.619196,MA0124.1;0.746208,MA0125.1;0.667416,MA0130.1;0,MA0131.1;0.345226,MA0132.1;0,MA0133.1;0,MA0135.1;0.588754,MA0136.1;0.260607,MA0139.1;0.0220308,MA0140.1;0.224213,MA0141.1;0.755821,MA0142.1;1.79298,MA0143.1;1.47497,MA0144.1;0.0449457,MA0145.1;0.00274371,MA0146.1;1.73108e-05,MA0147.1;0.204087,MA0148.1;0.198049,MA0149.1;0.21714,MA0062.2;0.0239298,MA0035.2;0.223695,MA0039.2;0.0017606,MA0138.2;0.331323,MA0002.2;0.294582,MA0137.2;0.0959012,MA0104.2;0.0336072,MA0047.2;0.277681,MA0112.2;0.0023312,MA0065.2;0.133665,MA0150.1;0.134443,MA0151.1;0,MA0152.1;0.648673,MA0153.1;0.65174,MA0154.1;0.00506877,MA0155.1;0.0128799,MA0156.1;0.0971366,MA0157.1;0.367703,MA0158.1;0,MA0159.1;0.0559104,MA0160.1;0.20889,MA0161.1;0,MA0162.1;0.000114726,MA0163.1;3.74282e-05,MA0164.1;0.310173,MA0080.2;0.0856322,MA0018.2;0.288301,MA0099.2;0.229319,MA0079.2;1.9383e-14,MA0102.2;1.07547,MA0258.1;0.160304,MA0259.1;0.0592752,MA0442.1;0}}
|full_id=C483_acute_diffuse_medulloblastoma_hepatocellular_small_mesothelioma_testicular
|gostat_on_coexpression_clusters=GO:0005938!cell cortex!0.0238210879547863!4691$GO:0008022!protein C-terminus binding!0.0238210879547863!4691$GO:0001525!angiogenesis!0.0238210879547863!4691$GO:0048514!blood vessel morphogenesis!0.0238210879547863!4691$GO:0048646!anatomical structure formation!0.0238210879547863!4691$GO:0001568!blood vessel development!0.0238210879547863!4691$GO:0005730!nucleolus!0.0238210879547863!4691$GO:0001944!vasculature development!0.0238210879547863!4691$GO:0009887!organ morphogenesis!0.0461752816044586!4691
|id=C483
}}

Latest revision as of 11:24, 17 September 2013


Full id: C483_acute_diffuse_medulloblastoma_hepatocellular_small_mesothelioma_testicular



Phase1 CAGE Peaks

Hg19::chr2:203160480..203160512,+p@chr2:203160480..203160512
+
Hg19::chr2:232323777..232323824,-p@chr2:232323777..232323824
-
Hg19::chr2:232324975..232325014,-p@chr2:232324975..232325014
-
Hg19::chr2:232325221..232325253,-p1@SNORD82
Hg19::chr2:232325265..232325286,-p2@SNORD82
Hg19::chr2:232325447..232325475,-p8@NCL
Hg19::chr2:232325476..232325496,-p13@NCL
Hg19::chr2:232325500..232325586,-p3@NCL
Hg19::chr2:232326295..232326310,-p10@NCL
Hg19::chr2:232326319..232326343,-p5@NCL
Hg19::chr2:232326429..232326440,-p11@NCL
Hg19::chr2:232326456..232326471,-p2@NCL
Hg19::chr2:232326479..232326493,-p6@NCL
Hg19::chr2:232326533..232326542,-p15@NCL
Hg19::chr2:232326600..232326609,-p12@NCL
Hg19::chr2:232326643..232326648,-p16@NCL
Hg19::chr2:232326697..232326708,-p9@NCL
Hg19::chr2:232326722..232326727,-p17@NCL
Hg19::chr2:232327965..232327986,-p21@NCL
Hg19::chr2:232327987..232328031,-p14@NCL


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:0005938cell cortex0.0238210879547863
GO:0008022protein C-terminus binding0.0238210879547863
GO:0001525angiogenesis0.0238210879547863
GO:0048514blood vessel morphogenesis0.0238210879547863
GO:0048646anatomical structure formation0.0238210879547863
GO:0001568blood vessel development0.0238210879547863
GO:0005730nucleolus0.0238210879547863
GO:0001944vasculature development0.0238210879547863
GO:0009887organ morphogenesis0.0461752816044586



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
disease of cellular proliferation5.38e-40239
cancer7.42e-40235
cell type cancer5.61e-21143
carcinoma1.28e-15106
organ system cancer1.98e-15137
hematologic cancer4.92e-1451
immune system cancer4.92e-1451
leukemia2.32e-1139
myeloid leukemia1.28e-0831


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)
MA0003.11.82551e-06
MA0004.10.180726
MA0006.10.0840255
MA0007.10.168078
MA0009.10.561062
MA0014.13.08855e-05
MA0017.10.105116
MA0019.11.43848
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.0924235
MA0029.13.12101
MA0030.10.474212
MA0031.10.41796
MA0038.10.25521
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.10.561349
MA0046.10.551181
MA0048.10.238801
MA0050.15.56259
MA0051.12.80282
MA0052.10.492957
MA0055.13.08726
MA0056.10
MA0057.10.00684412
MA0058.10.119655
MA0059.11.24352
MA0060.10.0338613
MA0061.10.0254296
MA0063.10
MA0066.10.255535
MA0067.10.858361
MA0068.10.614744
MA0069.10.547689
MA0070.10.537571
MA0071.10.22617
MA0072.10.533514
MA0073.16.97536e-08
MA0074.10.251422
MA0076.10.129195
MA0077.10.526569
MA0078.10.33032
MA0081.10.118989
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.10.0132273
MA0089.10
MA0090.10.138104
MA0091.10.182521
MA0092.10.157193
MA0093.10.0855877
MA0095.10
MA0098.10
MA0100.10.734012
MA0101.10.0872967
MA0103.11.99485
MA0105.10.00533645
MA0106.10.28721
MA0107.10.0527035
MA0108.20.415325
MA0109.10
MA0111.10.146643
MA0113.10.300221
MA0114.10.0506063
MA0115.11.84688
MA0116.11.17696
MA0117.10.595385
MA0119.10.109564
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.345226
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.0220308
MA0140.10.224213
MA0141.10.755821
MA0142.11.79298
MA0143.11.47497
MA0144.10.0449457
MA0145.10.00274371
MA0146.11.73108e-05
MA0147.10.204087
MA0148.10.198049
MA0149.10.21714
MA0062.20.0239298
MA0035.20.223695
MA0039.20.0017606
MA0138.20.331323
MA0002.20.294582
MA0137.20.0959012
MA0104.20.0336072
MA0047.20.277681
MA0112.20.0023312
MA0065.20.133665
MA0150.10.134443
MA0151.10
MA0152.10.648673
MA0153.10.65174
MA0154.10.00506877
MA0155.10.0128799
MA0156.10.0971366
MA0157.10.367703
MA0158.10
MA0159.10.0559104
MA0160.10.20889
MA0161.10
MA0162.10.000114726
MA0163.13.74282e-05
MA0164.10.310173
MA0080.20.0856322
MA0018.20.288301
MA0099.20.229319
MA0079.21.9383e-14
MA0102.21.07547
MA0258.10.160304
MA0259.10.0592752
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
POLR2A#5430192.040080517730175.50039674165619e-060.000166702244719045
SIX5#14791254.271678838864750.005067094740067110.0235945564919465
ZBTB33#1000957.916181257495290.0003267521810830770.00333063351943543
ZNF263#10127114.522012900355875.00671367500679e-060.000154565820131255



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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