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Coexpression cluster:C373: Difference between revisions

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{{Coexpression_clusters
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0.315775,0.483695,0.0158078,0.362804,0.012466,0.639649,0.129237,0.803555,0.128828,0.63368,0.670377,0.447678,0.2112,0.234335,0.222479,0.620243,0.722549,0.331692,0.870115,0.854198,0.814385,0.548322,0.793893,0.214215,0.365665,0.585646,0.588952,0.516042,0.000838621,0.946789,0.646123,0.410715,0.0778821,0.0630302,0.874218,0.30125,0.334328,0.445517,0.934837,0.27917,0.000415385,0.427186,0.880234,0.496272,0.806954,0.742877,0.163561,0.100506,0.544875,0.0126294,0.62679,0.887287,0.483215,0.958754,0.90736,0.563758,9.445e-05,0.664165,0.412918,0.413927,0.794821,0.543971,0.000789912,0.413698,0.173781,0.946775,0.899234,0.326011,0.118669,0.868889,0.55938,0.631478,0.473155,5.09242e-05,0.134568,0.656322,0.484904,0.179299,0.150358,0.672902,0.353439,0.488234,0.596475,0.303646,0.408715,0.647929,0.128147,0.633658,0.778992,0.771772,0.0791599,0.942617,0.884482,0.454923,0.66513,0.773355,0.849057,0.960231,0.796098,0.744821,0.504576,0.000521069,0.363279,0.837525,0.92632,0.00059391,0.695742,0.0343455,0.000236459,0.693951,0.877128,0.871115,0.397201,0.83124,0.765553,0.51875,0.914111,5.9654e-09,0.094394,0.707189,0.894776,0.254783,0.580421,0.711784,0.543326,0.812159,0.589921,0.509864,0.0890638,0.642801,0.0377206,0.845961,0.492364,0.904507,0.940217,0.0757001,0.986909|tfbs_overrepresentation_for_novel_motifs=1.64233,1.85282,1.60143,0.115973,0.0369893,0.115097,0.930842,0.143186,0.139834,0.736998,1.11439,0.545475,1.10306,0.901904,0.0365764,0.382537,1.51899,0.0973406,0.218375,0.465955,0.422633,0.690486,0.357972,0.59814,1.33816,0.5812,0.955628,1.73302,1.86417,0.241089,0.62111,0.341173,0.368873,0.817618,0.275894,0.548149,0.111654,0.115713,0.0923384,0.66459,0.273433,2.02011,0.184982,0.948411,0.845136,0.224432,0.480607,0.0941929,0.0440903,0.149585,0.603841,0.498457,0.40926,1.04005,0.532737,0.466119,0.0392903,0.82781,0.398965,1.93493,0.373766,0.484178,0.140489,0.291591,0.511492,0.266103,0.611096,0.954146,0.33304,0.800453,0.261495,0.0558475,11.5337,0.530988,2.18934,0.295725,0.137448,0.278987,0.330507,0.234869,0.228404,1.44032,0.171482,0.0109843,0.486416,1.78829,0.046923,0.0506093,1.20635,1.04966,0.695939,1.17096,0.354445,0.0170841,1.84848,0.0876739,0.215305,0.388689,0.653388,1.57962,0.232609,0.349965,0.384158,0.846519,2.84126,0.321489,0.303327,0.149517,0.24191,4.6794,1.18654,0.381914,0.411216,0.340192,0.652077,0.267503,0.170573,0.0883435,0.264397,0.394953,0.523757,0.226179,0.113636,0.178598,0.753832,0.27955,0.154657,0.942299,0.561176,0.424823,0.463953,0.0902711,0.573914,1.00462,0.707783,0.0135319,0.086099,0.11017,1.60526,1.49486,1.10037,0.634967,0.919194,0.385822,0.259011,0.405791,0.24704,1.33792,0.576539,2.16705,0.72532,8.7099,0.464277,0.129488,0.160304,0.829202,0.216727,0.133083,0.242284,0.208636,0.633868,0.448609,0.329893,0.464668,0.270734,0.170987,0.582013,0.157687,0.504522|tfbs_overrepresentation_jaspar=MA0003.1;0.777884,MA0004.1;1.66406,MA0006.1;0.952801,MA0007.1;0.309412,MA0009.1;0.429031,MA0014.1;0.138441,MA0017.1;0.729602,MA0019.1;0.188957,MA0024.1;0.343215,MA0025.1;0.544326,MA0027.1;1.97447,MA0028.1;0.160829,MA0029.1;0.358654,MA0030.1;0.922494,MA0031.1;0.809566,MA0038.1;0.160193,MA0040.1;0.363365,MA0041.1;0.111817,MA0042.1;0.0954223,MA0043.1;0.429296,MA0046.1;1.077,MA0048.1;3.38702,MA0050.1;0.0958601,MA0051.1;0.476736,MA0052.1;0.366488,MA0055.1;4.32836,MA0056.1;0,MA0057.1;0.0698664,MA0058.1;1.23175,MA0059.1;4.20617,MA0060.1;0.0511971,MA0061.1;0.105673,MA0063.1;0,MA0066.1;0.160456,MA0067.1;0.711124,MA0068.1;0.451179,MA0069.1;0.416668,MA0070.1;0.407339,MA0071.1;0.137013,MA0072.1;0.403605,MA0073.1;2.04749,MA0074.1;0.475593,MA0076.1;0.232584,MA0077.1;0.397221,MA0078.1;0.633683,MA0081.1;0.465159,MA0083.1;1.94488,MA0084.1;0.887042,MA0087.1;0.401577,MA0088.1;0.42613,MA0089.1;0,MA0090.1;0.250123,MA0091.1;0.103495,MA0092.1;0.287838,MA0093.1;0.965635,MA0095.1;0,MA0098.1;0,MA0100.1;0.168841,MA0101.1;0.150934,MA0103.1;1.31244,MA0105.1;0.0554264,MA0106.1;0.18641,MA0107.1;0.414244,MA0108.2;0.296685,MA0109.1;0,MA0111.1;0.266972,MA0113.1;0.197248,MA0114.1;0.400527,MA0115.1;0.640975,MA0116.1;0.0880779,MA0117.1;1.16571,MA0119.1;0.194128,MA0122.1;0.483183,MA0124.1;0.60338,MA0125.1;0.528543,MA0130.1;0,MA0131.1;0.23543,MA0132.1;0,MA0133.1;0,MA0135.1;0.454747,MA0136.1;0.493974,MA0139.1;5.45571,MA0140.1;0.833311,MA0141.1;0.210362,MA0142.1;0.755025,MA0143.1;0.573609,MA0144.1;2.60028,MA0145.1;0.343911,MA0146.1;2.31989,MA0147.1;4.68734,MA0148.1;0.115217,MA0149.1;0.129939,MA0062.2;0.0994414,MA0035.2;1.34622,MA0039.2;0.0326666,MA0138.2;0.635695,MA0002.2;0.124839,MA0137.2;1.48696,MA0104.2;4.99919,MA0047.2;0.178535,MA0112.2;0.632215,MA0065.2;0.0712417,MA0150.1;0.24291,MA0151.1;0,MA0152.1;0.849738,MA0153.1;0.513757,MA0154.1;0.69055,MA0155.1;1.25851,MA0156.1;0.385023,MA0157.1;0.708688,MA0158.1;0,MA0159.1;3.45722,MA0160.1;0.123537,MA0161.1;0,MA0162.1;0.123254,MA0163.1;0.223262,MA0164.1;0.205602,MA0080.2;0.342102,MA0018.2;1.04817,MA0099.2;0.431402,MA0079.2;0.00386036,MA0102.2;0.922526,MA0258.1;0.85521,MA0259.1;3.55156,MA0442.1;0}}
|full_id=C373_epidermoid_Prostate_cord_squamous_testicular_pharyngeal_testis
|id=C373
}}

Latest revision as of 11:21, 17 September 2013


Full id: C373_epidermoid_Prostate_cord_squamous_testicular_pharyngeal_testis



Phase1 CAGE Peaks

Hg19::chr10:134260508..134260546,+p@chr10:134260508..134260546
+
Hg19::chr11:69867159..69867175,-p3@ENST00000528507
Hg19::chr14:94405820..94405831,-p@chr14:94405820..94405831
-
Hg19::chr14:94405844..94405870,-p@chr14:94405844..94405870
-
Hg19::chr14:94405954..94405968,-p@chr14:94405954..94405968
-
Hg19::chr14:94405974..94405997,-p@chr14:94405974..94405997
-
Hg19::chr14:94406004..94406024,-p@chr14:94406004..94406024
-
Hg19::chr15:48442084..48442096,-p9@MYEF2
Hg19::chr17:34838949..34838959,-p@chr17:34838949..34838959
-
Hg19::chr17:39755734..39755747,-p@chr17:39755734..39755747
-
Hg19::chr17:39755914..39755961,-p@chr17:39755914..39755961
-
Hg19::chr20:43726566..43726571,+p@chr20:43726566..43726571
+
Hg19::chr20:43726572..43726588,+p@chr20:43726572..43726588
+
Hg19::chr20:43726947..43726954,-p@chr20:43726947..43726954
-
Hg19::chr20:43727145..43727152,-p@chr20:43727145..43727152
-
Hg19::chr20:43727168..43727209,-p@chr20:43727168..43727209
-
Hg19::chr20:43727212..43727217,-p@chr20:43727212..43727217
-
Hg19::chr20:57036925..57036961,-p9@APCDD1L
Hg19::chr2:99438974..99439027,-p5@C2orf55
Hg19::chr3:55205086..55205090,-p@chr3:55205086..55205090
-
Hg19::chr5:1882170..1882182,-p3@IRX4
Hg19::chr5:1882184..1882203,-p4@IRX4
Hg19::chr5:40984132..40984133,+p@chr5:40984132..40984133
+
Hg19::chr6:129597668..129597672,+p@chr6:129597668..129597672
+
Hg19::chr7:106101158..106101197,-p@chr7:106101158..106101197
-
Hg19::chr7:150871938..150871949,-p3@GBX1
Hg19::chr7:54900686..54900691,-p@chr7:54900686..54900691
-
Hg19::chrX:15683092..15683103,-p4@TMEM27
Hg19::chrX:15683147..15683159,-p3@TMEM27


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:0008241peptidyl-dipeptidase activity0.0314118382538923
GO:0004246peptidyl-dipeptidase A activity0.0314118382538923



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
epithelial cell of cervix1.55e-982
Uber Anatomy
Ontology termp-valuen
uterine epithelium1.55e-982
cervix epithelium1.55e-982
uterine cervix4.27e-346
neck of organ4.27e-346
uterus6.74e-1121
embryonic uterus1.80e-1022
internal female genitalia1.80e-1022
internal genitalia2.15e-0925
female reproductive organ8.21e-0737
female reproductive system8.21e-0737
Disease
Ontology termp-valuen
cervical cancer1.48e-405
squamous cell carcinoma1.43e-1514
female reproductive organ cancer8.32e-0927
reproductive organ cancer2.67e-0829


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)
MA0003.10.777884
MA0004.11.66406
MA0006.10.952801
MA0007.10.309412
MA0009.10.429031
MA0014.10.138441
MA0017.10.729602
MA0019.10.188957
MA0024.10.343215
MA0025.10.544326
MA0027.11.97447
MA0028.10.160829
MA0029.10.358654
MA0030.10.922494
MA0031.10.809566
MA0038.10.160193
MA0040.10.363365
MA0041.10.111817
MA0042.10.0954223
MA0043.10.429296
MA0046.11.077
MA0048.13.38702
MA0050.10.0958601
MA0051.10.476736
MA0052.10.366488
MA0055.14.32836
MA0056.10
MA0057.10.0698664
MA0058.11.23175
MA0059.14.20617
MA0060.10.0511971
MA0061.10.105673
MA0063.10
MA0066.10.160456
MA0067.10.711124
MA0068.10.451179
MA0069.10.416668
MA0070.10.407339
MA0071.10.137013
MA0072.10.403605
MA0073.12.04749
MA0074.10.475593
MA0076.10.232584
MA0077.10.397221
MA0078.10.633683
MA0081.10.465159
MA0083.11.94488
MA0084.10.887042
MA0087.10.401577
MA0088.10.42613
MA0089.10
MA0090.10.250123
MA0091.10.103495
MA0092.10.287838
MA0093.10.965635
MA0095.10
MA0098.10
MA0100.10.168841
MA0101.10.150934
MA0103.11.31244
MA0105.10.0554264
MA0106.10.18641
MA0107.10.414244
MA0108.20.296685
MA0109.10
MA0111.10.266972
MA0113.10.197248
MA0114.10.400527
MA0115.10.640975
MA0116.10.0880779
MA0117.11.16571
MA0119.10.194128
MA0122.10.483183
MA0124.10.60338
MA0125.10.528543
MA0130.10
MA0131.10.23543
MA0132.10
MA0133.10
MA0135.10.454747
MA0136.10.493974
MA0139.15.45571
MA0140.10.833311
MA0141.10.210362
MA0142.10.755025
MA0143.10.573609
MA0144.12.60028
MA0145.10.343911
MA0146.12.31989
MA0147.14.68734
MA0148.10.115217
MA0149.10.129939
MA0062.20.0994414
MA0035.21.34622
MA0039.20.0326666
MA0138.20.635695
MA0002.20.124839
MA0137.21.48696
MA0104.24.99919
MA0047.20.178535
MA0112.20.632215
MA0065.20.0712417
MA0150.10.24291
MA0151.10
MA0152.10.849738
MA0153.10.513757
MA0154.10.69055
MA0155.11.25851
MA0156.10.385023
MA0157.10.708688
MA0158.10
MA0159.13.45722
MA0160.10.123537
MA0161.10
MA0162.10.123254
MA0163.10.223262
MA0164.10.205602
MA0080.20.342102
MA0018.21.04817
MA0099.20.431402
MA0079.20.00386036
MA0102.20.922526
MA0258.10.85521
MA0259.13.55156
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
CTCF#10664142.587709973208630.0002781324296794360.00296165098116748
CTCFL#14069064.08547745358090.002917958086123570.015766393737734
ESR1#209966.36591792334230.000293096538099190.00310831735809721
MAX#4149153.337528711555416.20854210030502e-060.000183374979755021
RAD21#5885124.284841611912967.02264511834706e-060.000202775237355557
RXRA#625653.461140886057460.01336875009936690.0472397784418657
SMC3#912673.631535514294140.00242781388914580.0136770297625815
ZEB1#693563.494158348457350.006274603752039440.0276830576740135



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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