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Coexpression cluster:C513: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.514064268386681,0.37118002947767,0.39427933691332,0.016202029289334,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.188954912013133,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0226126326952331,0,0.146783911030037,0.135839138684319,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0575805665668305,0.132028466483572,0.199005448464995,0.140942333732381,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0171391479039887,0,0.0238730281222759,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.105739413005624,0,0,0,0,0,0,0.318841730269476,0.0209247759461169,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.170587479440239,0.66975035824777,1.11320804873573,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.206269694716997,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0543055354926695,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0545795660013852,0,0,0,0,0,0,0,0,0,0,0,0.341255153536293,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0754570760250905,0.0640596705171081,0,0,0.0574200118643566,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0591624956566136,0.0997390422089554,0,0,0,0,0,0,0,0,0.0557764781504105,0.0393578995913525,0,0,0.0490322556274006,0,0,0,0,0,0,0,0,0,0.0216030789840009,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0352989626615976,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0501432050255539,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.214404368077712,0,0,0,0,0,0,0,0,0,0,0,0,0.157176350930889,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0832560638586098,0,0,0,0,0,0,0,0,0,0.0317165860483832,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0484300422256687,0.135723143846782,0.178963825975293,0,0,0,0,0,0,0,0.065867873206635,0.0598874413026267,0,0,0,0,0,0,0,0,0.196903961995475,0,0,0,0,0,0.0473659963914933,0,0,0,0,0.0665200795367872,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0713494635703484,0.467700405247217,0,0,0,0,0,0,0,0,0,0,0,0,0.0450355340939671,0,0,0,0,0,0,0,0,0,0,0,0,0,0.177117418991982,0,0,0,0,0,0,0,0.122416778853372,0,0,0,0,0,0,0,0,0|full_id=C513_Tracheal_Bronchial_squamous_bronchial_Small_oral_medulloblastoma|gostat_on_coexpression_clusters=GO:0030160!GKAP/Homer scaffold activity!0.00557297107210372!22941$GO:0000085!G2 phase of mitotic cell cycle!0.00557297107210372!1112$GO:0051319!G2 phase!0.00557297107210372!1112$GO:0030159!receptor signaling complex scaffold activity!0.0167130071253003!22941$GO:0032947!protein complex scaffold!0.0167130071253003!22941$GO:0000077!DNA damage checkpoint!0.0167130071253003!1112$GO:0031570!DNA integrity checkpoint!0.0167130071253003!1112$GO:0042770!DNA damage response, signal transduction!0.0224531431309998!1112$GO:0000075!cell cycle checkpoint!0.0259872926223361!1112$GO:0051329!interphase of mitotic cell 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.541619,0.326996,0.48466,0.337521,0.378673,0.56258,0.15359,0.237135,0.340182,0.430665,0.201185,0.581027,0.746375,0.878019,0.868276,0.922494,0.600289,0.839955,0.830335,0.738063,0.458329,0.35741,0.523407,0.690759,0.86487,0.28079,0.571615,0.650351,0.749886,0.38488,0.601711,0.801858,0.682653,0.0389982,0.771405,0.44895,0.520448,0.727834,0.719642,0.862678,0.593425,0.249584,0.2934,0.197101,0.445395,0.217442,0.784583,0.752806,0.453778,0.102276,0.898367,0.677018,0.645799,0.295944,0.357633,0.294452,0.472167,0.779178,0.686837,0.641805,0.0604603,0.255632,0.749347,0.749736|tfbs_overrepresentation_for_novel_motifs=0.132318,0.114322,0.799632,0.642587,0.10302,0.63973,0.283394,0.691671,0.384015,0.327423,0.203249,0.318077,0.288598,0.753523,1.13295,0.115805,0.469711,0.546349,0.134253,0.917145,0.401545,0.0543058,0.219533,0.329158,0.156949,0.336616,1.0959,0.217946,0.104779,0.214203,0.187767,0.502277,0.212656,0.123119,0.0841935,0.283823,0.0825354,0.2261,0.905465,0.0376222,0.283797,0.523145,0.280758,0.332492,0.222476,0.147132,0.284252,0.195517,0.875099,0.341709,0.348337,0.293583,0.502427,0.571408,0.712611,0.276665,0.707757,0.251346,0.0845735,0.250577,0.538962,0.286121,0.385159,0.445454,0.300385,0.415664,0.795966,1.15172,0.493047,0.993712,0.167519,0.712355,0.0516651,0.710737,0.115969,0.252901,0.70408,1.10062,0.490165,0.152902,0.326109,0.444519,0.300103,0.701851,0.662744,0.0432732,0.00709181,0.652631,0.967962,1.24919,0.885103,0.637733,0.517273,0.482989,0.103441,0.239995,0.132621,0.555608,0.976491,0.0141994,0.25011,0.512221,0.550563,0.472938,0.405789,0.200011,0.45903,0.27168,0.156782,0.0941477,0.134708,0.548062,0.124365,0.210038,0.839147,0.278955,0.126573,0.186928,0.413654,0.226032,0.702982,0.963474,0.22321,0.309149,0.945405,0.431436,0.278404,0.521744,0.742996,0.517952,0.638371,0.555366,0.756554,0.826375,0.897471,0.375295,1.63395,0.21836,0.856781,1.69932,1.30076,0.82115,0.765828,0.552418,0.407293,0.244914,0.393075,1.5412,0.174198,0.217844,0.447514,0.00309082,0.638724,0.0412184,0.285738,1.0234,1.6742,0.315972,0.156987,0.13835,0.819992,0.621644,0.489467,0.140388,0.421111,0.299472,0.445457,0.771721,0.00699698|tfbs_overrepresentation_jaspar=MA0003.1;0.00101787,MA0004.1;0.596623,MA0006.1;0.101986,MA0007.1;0.193512,MA0009.1;0.600198,MA0014.1;0.00375206,MA0017.1;0.125342,MA0019.1;0.861701,MA0024.1;0.50459,MA0025.1;0.725013,MA0027.1;2.18072,MA0028.1;0.358818,MA0029.1;0.522011,MA0030.1;0.511665,MA0031.1;0.454061,MA0038.1;1.42144,MA0040.1;1.3076,MA0041.1;1.17879,MA0042.1;1.08781,MA0043.1;0.60049,MA0046.1;0.590147,MA0048.1;0.0114521,MA0050.1;0.197941,MA0051.1;0.282227,MA0052.1;0.530811,MA0055.1;0.231394,MA0056.1;0,MA0057.1;0.141662,MA0058.1;0.435867,MA0059.1;0.854645,MA0060.1;0.0444001,MA0061.1;1.32241,MA0063.1;0,MA0066.1;0.779889,MA0067.1;0.900956,MA0068.1;0.0967272,MA0069.1;0.586593,MA0070.1;0.576293,MA0071.1;0.709276,MA0072.1;0.572162,MA0073.1;4.73229e-07,MA0074.1;0.281628,MA0076.1;0.461922,MA0077.1;0.565087,MA0078.1;0.954093,MA0081.1;0.140536,MA0083.1;0.607144,MA0084.1;1.08294,MA0087.1;0.569916,MA0088.1;0.673545,MA0089.1;0,MA0090.1;0.161293,MA0091.1;0.601165,MA0092.1;0.53622,MA0093.1;0.691334,MA0095.1;0,MA0098.1;0,MA0100.1;0.296726,MA0101.1;0.700148,MA0103.1;1.09511,MA0105.1;1.30924,MA0106.1;1.54181,MA0107.1;0.871747,MA0108.2;0.451357,MA0109.1;0,MA0111.1;0.170509,MA0113.1;0.332535,MA0114.1;0.228885,MA0115.1;0.827474,MA0116.1;0.240715,MA0117.1;0.635078,MA0119.1;0.130226,MA0122.1;0.659244,MA0124.1;0.787807,MA0125.1;0.708116,MA0130.1;0,MA0131.1;0.379172,MA0132.1;0,MA0133.1;0,MA0135.1;0.628343,MA0136.1;0.291242,MA0139.1;0.0300305,MA0140.1;0.253051,MA0141.1;0.430939,MA0142.1;0.426146,MA0143.1;0.885144,MA0144.1;0.209582,MA0145.1;0.175315,MA0146.1;0.050005,MA0147.1;0.245602,MA0148.1;0.640121,MA0149.1;0.245595,MA0062.2;0.131354,MA0035.2;0.703256,MA0039.2;0.0239272,MA0138.2;0.364793,MA0002.2;0.999186,MA0137.2;0.368913,MA0104.2;0.383074,MA0047.2;0.309071,MA0112.2;0.0229828,MA0065.2;0.526971,MA0150.1;0.157331,MA0151.1;0,MA0152.1;0.716282,MA0153.1;0.692238,MA0154.1;0.117204,MA0155.1;0.0203861,MA0156.1;0.372479,MA0157.1;0.402372,MA0158.1;0,MA0159.1;0.527394,MA0160.1;0.666979,MA0161.1;0,MA0162.1;0.0280426,MA0163.1;0.000900095,MA0164.1;0.342871,MA0080.2;0.338854,MA0018.2;0.320136,MA0099.2;1.32148,MA0079.2;0.00196147,MA0102.2;1.11935,MA0258.1;0.053266,MA0259.1;0.257452,MA0442.1;0}}
|full_id=C513_Tracheal_Bronchial_squamous_bronchial_Small_oral_medulloblastoma
|gostat_on_coexpression_clusters=GO:0030160!GKAP/Homer scaffold activity!0.00557297107210372!22941$GO:0000085!G2 phase of mitotic cell cycle!0.00557297107210372!1112$GO:0051319!G2 phase!0.00557297107210372!1112$GO:0030159!receptor signaling complex scaffold activity!0.0167130071253003!22941$GO:0032947!protein complex scaffold!0.0167130071253003!22941$GO:0000077!DNA damage checkpoint!0.0167130071253003!1112$GO:0031570!DNA integrity checkpoint!0.0167130071253003!1112$GO:0042770!DNA damage response, signal transduction!0.0224531431309998!1112$GO:0000075!cell cycle checkpoint!0.0259872926223361!1112$GO:0051329!interphase of mitotic cell cycle!0.0341544880708405!1112$GO:0051325!interphase!0.0341544880708405!1112
|id=C513
|ontology_enrichment_celltype=CL:0000066!2.00e-26!254;CL:0002321!2.67e-15!248;CL:0000220!1.10e-14!246;CL:0002076!3.41e-13!43;CL:0000223!1.38e-12!59;CL:0000012!1.41e-09!682;CL:0000548!1.91e-09!679;CL:0000004!1.91e-09!679;CL:0000255!1.91e-09!679;CL:0002368!9.21e-09!13;CL:0000221!7.78e-08!71;CL:0002202!4.20e-07!9;CL:0002632!4.20e-07!9
|ontology_enrichment_disease=DOID:162!6.70e-26!235;DOID:14566!7.84e-26!239;DOID:0050687!1.39e-23!143;DOID:305!9.09e-22!106;DOID:1749!3.06e-08!14;DOID:0050686!6.44e-08!137
|ontology_enrichment_uberon=UBERON:0004119!1.29e-07!169;UBERON:0000925!1.29e-07!169;UBERON:0006595!1.29e-07!169;UBERON:0001004!1.49e-07!72;UBERON:0003102!2.01e-07!95;UBERON:0003104!2.59e-07!238;UBERON:0009142!2.59e-07!238
}}

Latest revision as of 11:24, 17 September 2013


Full id: C513_Tracheal_Bronchial_squamous_bronchial_Small_oral_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr11:70952310..70952311,-p24@SHANK2
Hg19::chr14:90085820..90085840,-p6@FOXN3
Hg19::chr15:76443020..76443024,-p@chr15:76443020..76443024
-
Hg19::chr17:80450992..80450999,+p@chr17:80450992..80450999
+
Hg19::chr1:150254401..150254408,-p@chr1:150254401..150254408
-
Hg19::chr1:185381713..185381720,-p@chr1:185381713..185381720
-
Hg19::chr1:200270929..200270934,-p@chr1:200270929..200270934
-
Hg19::chr1:3591362..3591369,-p@chr1:3591362..3591369
-
Hg19::chr20:6902511..6902515,+p@chr20:6902511..6902515
+
Hg19::chr3:134049971..134049973,-p@chr3:134049971..134049973
-
Hg19::chr3:37262958..37262962,+p@chr3:37262958..37262962
+
Hg19::chr4:44963669..44963674,+p@chr4:44963669..44963674
+
Hg19::chr5:138751193..138751196,-p@chr5:138751193..138751196
-
Hg19::chr5:34599678..34599683,-p@chr5:34599678..34599683
-
Hg19::chr7:46608530..46608534,+p@chr7:46608530..46608534
+
Hg19::chr8:126557025..126557029,+p@chr8:126557025..126557029
+
Hg19::chr8:98941240..98941249,+p@chr8:98941240..98941249
+
Hg19::chr8:99403902..99403910,+p@chr8:99403902..99403910
+


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:0030160GKAP/Homer scaffold activity0.00557297107210372
GO:0000085G2 phase of mitotic cell cycle0.00557297107210372
GO:0051319G2 phase0.00557297107210372
GO:0030159receptor signaling complex scaffold activity0.0167130071253003
GO:0032947protein complex scaffold0.0167130071253003
GO:0000077DNA damage checkpoint0.0167130071253003
GO:0031570DNA integrity checkpoint0.0167130071253003
GO:0042770DNA damage response, signal transduction0.0224531431309998
GO:0000075cell cycle checkpoint0.0259872926223361
GO:0051329interphase of mitotic cell cycle0.0341544880708405
GO:0051325interphase0.0341544880708405



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>

Disease
Ontology termp-valuen
squamous cell carcinoma4.37e-2714
carcinoma3.11e-11106
cell type cancer6.82e-09143
cancer2.07e-08235
disease of cellular proliferation4.29e-08239


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)
MA0003.10.00101787
MA0004.10.596623
MA0006.10.101986
MA0007.10.193512
MA0009.10.600198
MA0014.10.00375206
MA0017.10.125342
MA0019.10.861701
MA0024.10.50459
MA0025.10.725013
MA0027.12.18072
MA0028.10.358818
MA0029.10.522011
MA0030.10.511665
MA0031.10.454061
MA0038.11.42144
MA0040.11.3076
MA0041.11.17879
MA0042.11.08781
MA0043.10.60049
MA0046.10.590147
MA0048.10.0114521
MA0050.10.197941
MA0051.10.282227
MA0052.10.530811
MA0055.10.231394
MA0056.10
MA0057.10.141662
MA0058.10.435867
MA0059.10.854645
MA0060.10.0444001
MA0061.11.32241
MA0063.10
MA0066.10.779889
MA0067.10.900956
MA0068.10.0967272
MA0069.10.586593
MA0070.10.576293
MA0071.10.709276
MA0072.10.572162
MA0073.14.73229e-07
MA0074.10.281628
MA0076.10.461922
MA0077.10.565087
MA0078.10.954093
MA0081.10.140536
MA0083.10.607144
MA0084.11.08294
MA0087.10.569916
MA0088.10.673545
MA0089.10
MA0090.10.161293
MA0091.10.601165
MA0092.10.53622
MA0093.10.691334
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.10.700148
MA0103.11.09511
MA0105.11.30924
MA0106.11.54181
MA0107.10.871747
MA0108.20.451357
MA0109.10
MA0111.10.170509
MA0113.10.332535
MA0114.10.228885
MA0115.10.827474
MA0116.10.240715
MA0117.10.635078
MA0119.10.130226
MA0122.10.659244
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.291242
MA0139.10.0300305
MA0140.10.253051
MA0141.10.430939
MA0142.10.426146
MA0143.10.885144
MA0144.10.209582
MA0145.10.175315
MA0146.10.050005
MA0147.10.245602
MA0148.10.640121
MA0149.10.245595
MA0062.20.131354
MA0035.20.703256
MA0039.20.0239272
MA0138.20.364793
MA0002.20.999186
MA0137.20.368913
MA0104.20.383074
MA0047.20.309071
MA0112.20.0229828
MA0065.20.526971
MA0150.10.157331
MA0151.10
MA0152.10.716282
MA0153.10.692238
MA0154.10.117204
MA0155.10.0203861
MA0156.10.372479
MA0157.10.402372
MA0158.10
MA0159.10.527394
MA0160.10.666979
MA0161.10
MA0162.10.0280426
MA0163.10.000900095
MA0164.10.342871
MA0080.20.338854
MA0018.20.320136
MA0099.21.32148
MA0079.20.00196147
MA0102.21.11935
MA0258.10.053266
MA0259.10.257452
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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