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Coexpression cluster:C571: Difference between revisions

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{{Coexpression_clusters
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,0.0364248,0.035203|tfbs_overrepresentation_for_novel_motifs=0.928065,0.621887,0.464859,0.258928,1.28612,0.25764,0.854181,0.215354,0.463955,0.143512,0.660906,0.355038,0.0400361,0.309388,0.124662,0.851457,0.511522,0.639388,0.388593,0.520625,0.152859,0.765208,0.701134,0.387475,0.542899,0.977358,1.28796,0.249905,0.400769,0.815202,0.622094,0.544857,0.552347,0.15896,0.104423,0.579385,0.102549,0.258546,0.299553,0.0503272,0.690753,0.205653,2.34035,0.391064,0.321633,0.517036,0.856196,1.19938,0.541305,0.798822,0.386472,0.878028,0.625622,0.615394,0.758742,0.311792,0.407898,0.2852,0.274137,0.284391,1.42397,0.321692,0.465207,0.48664,0.336598,0.456015,0.843028,1.20113,1.32482,1.04233,0.19602,0.0621482,0.0732084,0.756844,0.150647,0.580064,0.288432,1.18857,0.532468,0.18023,0.177931,0.48568,0.336303,0.82567,0.70821,0.0705689,0.149619,1.56962,0.408949,1.29895,0.932961,0.68283,0.560183,0.0788172,0.12599,0.60642,1.05857,0.599297,0.412954,2.89988,0.301599,0.555021,0.594155,0.514828,0.445845,0.230832,0.500571,0.306566,0.18443,0.115618,0.48378,0.591605,0.455599,0.241506,0.886618,0.333119,0.318047,0.619973,0.453946,0.578957,0.748992,0.406842,0.255485,0.914205,0.993708,1.19002,0.313614,0.564749,0.78949,0.291925,0.683478,0.219902,0.803201,0.342946,0.945426,0.101403,0.611533,0.698255,0.904406,1.74999,1.35069,0.868456,0.315034,1.45285,0.447394,0.278424,1.10486,1.59165,1.11101,0.0770919,0.564239,0.0298174,0.683836,0.443914,0.321292,1.07219,0.394947,0.373254,0.543,0.164414,0.867287,0.66649,0.531753,0.499061,1.1672,0.335644,0.0708512,0.317742,0.297192|tfbs_overrepresentation_jaspar=MA0003.1;0.357653,MA0004.1;0.238283,MA0006.1;0.124371,MA0007.1;0.636564,MA0009.1;0.644692,MA0014.1;0.446753,MA0017.1;0.150184,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.419336,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;1.54944,MA0040.1;0.570428,MA0041.1;0.252793,MA0042.1;0.227947,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.390294,MA0050.1;0.228625,MA0051.1;0.317617,MA0052.1;0.574006,MA0055.1;0.499384,MA0056.1;0,MA0057.1;0.0733461,MA0058.1;0.167587,MA0059.1;0.166682,MA0060.1;0.0584466,MA0061.1;0.0461955,MA0063.1;0,MA0066.1;1.55071,MA0067.1;0.948938,MA0068.1;0.880335,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;0.616162,MA0073.1;0.280303,MA0074.1;0.850035,MA0076.1;0.178863,MA0077.1;0.608956,MA0078.1;0.402443,MA0081.1;0.166796,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;1.15536,MA0089.1;0,MA0090.1;0.554239,MA0091.1;0.240316,MA0092.1;1.78877,MA0093.1;0.12631,MA0095.1;0,MA0098.1;0,MA0100.1;0.332778,MA0101.1;0.128426,MA0103.1;0.75875,MA0105.1;0.0621554,MA0106.1;0.355999,MA0107.1;0.285979,MA0108.2;0.492699,MA0109.1;0,MA0111.1;0.199239,MA0113.1;0.370073,MA0114.1;0.0814649,MA0115.1;0.874839,MA0116.1;0.291279,MA0117.1;0.680135,MA0119.1;0.918526,MA0122.1;0.70466,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;0.418384,MA0132.1;0,MA0133.1;0,MA0135.1;0.673296,MA0136.1;0.87256,MA0139.1;0.159457,MA0140.1;0.7823,MA0141.1;0.165463,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.0738381,MA0145.1;0.23881,MA0146.1;0.528155,MA0147.1;0.0881384,MA0148.1;0.257816,MA0149.1;0.279141,MA0062.2;0.0439512,MA0035.2;0.286421,MA0039.2;0.217508,MA0138.2;0.403517,MA0002.2;0.434729,MA0137.2;0.138998,MA0104.2;0.0580852,MA0047.2;0.345656,MA0112.2;0.22067,MA0065.2;0.0416912,MA0150.1;1.03901,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;0.820684,MA0155.1;0.837529,MA0156.1;0.433955,MA0157.1;0.442323,MA0158.1;0,MA0159.1;0.619098,MA0160.1;0.26995,MA0161.1;0,MA0162.1;0.104382,MA0163.1;0.324683,MA0164.1;0.99163,MA0080.2;0.793571,MA0018.2;0.357181,MA0099.2;0.292649,MA0079.2;0.23065,MA0102.2;1.16862,MA0258.1;0.520754,MA0259.1;0.0929051,MA0442.1;0}}
|full_id=C571_Bronchial_Prostate_Small_Tracheal_Mallassezderived_Urothelial_Gingival
|id=C571
|ontology_enrichment_celltype=CL:0000066!4.64e-28!254;CL:0002076!2.15e-19!43;CL:0000223!1.59e-16!59;CL:0002368!1.18e-09!13;CL:0002251!7.05e-08!21;CL:0002202!7.39e-07!9;CL:0002632!7.39e-07!9
|ontology_enrichment_disease=DOID:305!1.34e-13!106;DOID:0050687!2.00e-10!143;DOID:299!1.08e-08!25;DOID:1749!5.67e-07!14
|ontology_enrichment_uberon=UBERON:0000062!1.63e-17!511;UBERON:0004119!8.72e-16!169;UBERON:0000925!8.72e-16!169;UBERON:0006595!8.72e-16!169;UBERON:0002050!1.93e-11!605;UBERON:0005423!1.93e-11!605;UBERON:0000468!2.42e-11!659;UBERON:0000923!3.01e-11!604;UBERON:0005291!3.01e-11!604;UBERON:0006598!3.01e-11!604;UBERON:0002532!3.01e-11!604;UBERON:0000467!3.35e-11!625;UBERON:0000480!5.22e-11!626;UBERON:0001007!6.91e-11!155;UBERON:0001555!6.91e-11!155;UBERON:0007026!6.91e-11!155;UBERON:0000922!1.01e-10!612;UBERON:0001004!6.65e-10!72;UBERON:0000077!1.36e-09!130;UBERON:0004921!4.74e-09!129;UBERON:0004185!4.74e-09!129;UBERON:0000064!8.20e-09!219;UBERON:0000464!5.65e-08!104;UBERON:0000065!1.50e-07!53;UBERON:0005631!2.13e-07!14;UBERON:0000158!2.13e-07!14;UBERON:0001041!3.62e-07!98;UBERON:0008947!6.80e-07!38;UBERON:0003258!6.80e-07!38
}}

Latest revision as of 11:26, 17 September 2013


Full id: C571_Bronchial_Prostate_Small_Tracheal_Mallassezderived_Urothelial_Gingival



Phase1 CAGE Peaks

Hg19::chr17:73724438..73724471,+p@chr17:73724438..73724471
+
Hg19::chr17:73725353..73725387,+p@chr17:73725353..73725387
+
Hg19::chr17:73726320..73726332,+p@chr17:73726320..73726332
+
Hg19::chr1:183177006..183177041,+p@chr1:183177006..183177041
+
Hg19::chr1:183177076..183177103,+p@chr1:183177076..183177103
+
Hg19::chr1:209790813..209790826,-p@chr1:209790813..209790826
-
Hg19::chr1:209796354..209796366,-p@chr1:209796354..209796366
-
Hg19::chr1:209800857..209800874,-p@chr1:209800857..209800874
-
Hg19::chr1:209801414..209801425,-p@chr1:209801414..209801425
-
Hg19::chr1:209806051..209806064,-p@chr1:209806051..209806064
-
Hg19::chr1:209806472..209806488,-p@chr1:209806472..209806488
-
Hg19::chr1:209807970..209807983,-p@chr1:209807970..209807983
-
Hg19::chr1:209823365..209823389,-p@chr1:209823365..209823389
-
Hg19::chr1:209823405..209823427,-p@chr1:209823405..209823427
-
Hg19::chr1:209823455..209823467,-p@chr1:209823455..209823467
-
Hg19::chr20:388836..388841,+p8@RBCK1


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

No GOStat results

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
endo-epithelial cell6.45e-4742
epithelial cell5.95e-37253
endodermal cell2.21e-3158
respiratory epithelial cell2.99e-2213
epithelial cell of alimentary canal3.67e-2220
general ecto-epithelial cell1.58e-1614
epithelial cell of tracheobronchial tree1.99e-139
epithelial cell of lower respiratory tract1.99e-139
transitional epithelial cell4.92e-114
urothelial cell4.92e-114
ecto-epithelial cell1.69e-0934
embryonic cell2.04e-09250
bronchial epithelial cell7.27e-093
duct epithelial cell1.29e-083
branched duct epithelial cell1.29e-083
tracheal epithelial cell1.29e-083
tracheoblast1.29e-083
epithelial cell of Malassez1.96e-083
squamous epithelial cell2.00e-0863
gingival epithelial cell2.33e-083
extraembryonic cell2.63e-0819
epithelial cell of prostate3.78e-083
chorionic membrane mesenchymal stem cell2.03e-073
acinar cell2.06e-075
epithelial cell of stomach3.41e-073
stratified squamous epithelial cell4.31e-076
keratin accumulating cell4.31e-076
stratified epithelial cell4.31e-076
keratinizing barrier epithelial cell4.31e-076
epithelial fate stem cell4.31e-076
stratified epithelial stem cell4.31e-076
surface ectodermal cell4.31e-076
epidermal cell5.91e-079
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.20e-16160
endoderm2.20e-16160
presumptive endoderm2.20e-16160
urothelium8.50e-135
extraembryonic membrane6.44e-1214
membranous layer6.44e-1214
transitional epithelium1.40e-106
tracheobronchial tree1.82e-0915
lower respiratory tract1.82e-0915
digestive system4.78e-09145
digestive tract4.78e-09145
primitive gut4.78e-09145
lower respiratory tract epithelium7.27e-093
epithelium of bronchus7.27e-093
respiratory system7.28e-0974
surface structure1.86e-0899
gingival epithelium2.33e-083
mouth mucosa3.15e-0813
chorion5.83e-087
mucosa7.03e-0820
orifice7.13e-0836
acellular anatomical structure2.03e-073
egg chorion2.03e-073
endo-epithelium2.12e-0782
epithelium of mucosa3.15e-078
epithelial fold6.23e-0747
organ component layer6.79e-0766
epithelial bud7.21e-0737
subdivision of digestive tract7.42e-07118
Disease
Ontology termp-valuen
squamous cell carcinoma1.04e-1314
carcinoma4.99e-07106


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)
MA0003.10.357653
MA0004.10.238283
MA0006.10.124371
MA0007.10.636564
MA0009.10.644692
MA0014.10.446753
MA0017.10.150184
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.419336
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.11.54944
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.390294
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.499384
MA0056.10
MA0057.10.0733461
MA0058.10.167587
MA0059.10.166682
MA0060.10.0584466
MA0061.10.0461955
MA0063.10
MA0066.11.55071
MA0067.10.948938
MA0068.10.880335
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.280303
MA0074.10.850035
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.166796
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.11.15536
MA0089.10
MA0090.10.554239
MA0091.10.240316
MA0092.11.78877
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.128426
MA0103.10.75875
MA0105.10.0621554
MA0106.10.355999
MA0107.10.285979
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.10.0814649
MA0115.10.874839
MA0116.10.291279
MA0117.10.680135
MA0119.10.918526
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.87256
MA0139.10.159457
MA0140.10.7823
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.0738381
MA0145.10.23881
MA0146.10.528155
MA0147.10.0881384
MA0148.10.257816
MA0149.10.279141
MA0062.20.0439512
MA0035.20.286421
MA0039.20.217508
MA0138.20.403517
MA0002.20.434729
MA0137.20.138998
MA0104.20.0580852
MA0047.20.345656
MA0112.20.22067
MA0065.20.0416912
MA0150.11.03901
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.820684
MA0155.10.837529
MA0156.10.433955
MA0157.10.442323
MA0158.10
MA0159.10.619098
MA0160.10.26995
MA0161.10
MA0162.10.104382
MA0163.10.324683
MA0164.10.99163
MA0080.20.793571
MA0018.20.357181
MA0099.20.292649
MA0079.20.23065
MA0102.21.16862
MA0258.10.520754
MA0259.10.0929051
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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