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Coexpression cluster:C225: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0235254,9.40086e-05,0.00364314,0.412537,1.62608,0.993059,0.587726,1.72217,0.150614,0.00337409,0.0140873,0.175407,0.0756698,0.305159,1.61445,0.847271,0.116178,1.17736,0.0944627,0.0430066,1.608,0.0147742,0.0174359,1.25664,0.0359859,0.0531621,0.0242726,0.0778953,0.0128454,0.112488,0.149684,0.13466,0.00255642,0.0406029,0.0262566,0.0604798,0.000937776,0.0845975,0.102101,0.00342061,0.786172,0.132333,0.214327,0.504826,0.00719521,0.00555999,0.138997,0.0126371,0.236991,0.204272,0.0578181,0.148717,0.046072,0.177258,0.276099,0.0323524,1.68997,0.106844,0.0161288,0.106134,0.474575,0.0352913,0.367379,0.103136,0.0399717,0.616779,0.340363,0.646263,0.405475,0.505394,0.0081297,0.560383,8.81891e-07,0.274699,0.00548702,0.00100571,0.290824,0.0955607,0.12766,1.52518,0.537554,0.335838,3.64838,0.0913969,0.239598,7.2862e-06,0.236292,0.243422,0.237141,0.735915,0.412856,0.63189,0.867865,0.385152,0.00190761,0.288541,0.246063,0.500313,0.519218,0.00876336,0.190195,0.140514,0.16396,0.11796,0.0832359,0.0134689,0.110356,0.126312,0.104056,0.00142168,0.075669,0.488603,0.0636913,0.07163,0.375043,0.553118,2.8106e-05,0.0111312,0.0870355,0.155081,0.268929,0.234602,0.40297,0.376466,0.46373,0.317735,0.133036,0.146211,0.299084,0.17704,1.18527,0.794075,0.309508,0.162553,0.423179,0.71855,0.0524356,0.3888,0.389447,1.16613,0.784022,0.360483,0.576162,0.165128,0.285147,0.248347,0.266485,1.0128,0.266075,0.00278411,0.0160927,6.24145e-05,0.222603,0.000913465,0.935098,0.531361,0.0611763,0.463932,0.104338,0.00463012,0.359552,0.210769,0.127261,0.329311,1.05273,0.154981,0.0272775,0.137043,1.56676e-09
|tfbs_overrepresentation_for_novel_motifs=0.0235254,9.40086e-05,0.00364314,0.412537,1.62608,0.993059,0.587726,1.72217,0.150614,0.00337409,0.0140873,0.175407,0.0756698,0.305159,1.61445,0.847271,0.116178,1.17736,0.0944627,0.0430066,1.608,0.0147742,0.0174359,1.25664,0.0359859,0.0531621,0.0242726,0.0778953,0.0128454,0.112488,0.149684,0.13466,0.00255642,0.0406029,0.0262566,0.0604798,0.000937776,0.0845975,0.102101,0.00342061,0.786172,0.132333,0.214327,0.504826,0.00719521,0.00555999,0.138997,0.0126371,0.236991,0.204272,0.0578181,0.148717,0.046072,0.177258,0.276099,0.0323524,1.68997,0.106844,0.0161288,0.106134,0.474575,0.0352913,0.367379,0.103136,0.0399717,0.616779,0.340363,0.646263,0.405475,0.505394,0.0081297,0.560383,8.81891e-07,0.274699,0.00548702,0.00100571,0.290824,0.0955607,0.12766,1.52518,0.537554,0.335838,3.64838,0.0913969,0.239598,7.2862e-06,0.236292,0.243422,0.237141,0.735915,0.412856,0.63189,0.867865,0.385152,0.00190761,0.288541,0.246063,0.500313,0.519218,0.00876336,0.190195,0.140514,0.16396,0.11796,0.0832359,0.0134689,0.110356,0.126312,0.104056,0.00142168,0.075669,0.488603,0.0636913,0.07163,0.375043,0.553118,2.8106e-05,0.0111312,0.0870355,0.155081,0.268929,0.234602,0.40297,0.376466,0.46373,0.317735,0.133036,0.146211,0.299084,0.17704,1.18527,0.794075,0.309508,0.162553,0.423179,0.71855,0.0524356,0.3888,0.389447,1.16613,0.784022,0.360483,0.576162,0.165128,0.285147,0.248347,0.266485,1.0128,0.266075,0.00278411,0.0160927,6.24145e-05,0.222603,0.000913465,0.935098,0.531361,0.0611763,0.463932,0.104338,0.00463012,0.359552,0.210769,0.127261,0.329311,1.05273,0.154981,0.0272775,0.137043,1.56676e-09
|tfbs_overrepresentation_jaspar=MA0003.1;1.68077e-11,MA0004.1;0.59382,MA0006.1;0.0409568,MA0007.1;0.158809,MA0009.1;0.196219,MA0014.1;1.87231e-10,MA0017.1;0.0647838,MA0019.1;0.404253,MA0024.1;0.136013,MA0025.1;0.778709,MA0027.1;1.64023,MA0028.1;0.0150707,MA0029.1;0.146371,MA0030.1;0.433144,MA0031.1;0.349229,MA0038.1;0.934456,MA0040.1;0.149577,MA0041.1;2.22512,MA0042.1;3.51029,MA0043.1;0.57133,MA0046.1;0.189523,MA0048.1;0.0869886,MA0050.1;0.0625073,MA0051.1;0.136921,MA0052.1;0.462101,MA0055.1;0.000300352,MA0056.1;0,MA0057.1;0.000422302,MA0058.1;0.332561,MA0059.1;0.18173,MA0060.1;0.36689,MA0061.1;0.00911456,MA0063.1;0,MA0066.1;0.935977,MA0067.1;0.426099,MA0068.1;0.143048,MA0069.1;0.187175,MA0070.1;0.53276,MA0071.1;0.799731,MA0072.1;0.177746,MA0073.1;0.0292881,MA0074.1;0.13631,MA0076.1;0.0330734,MA0077.1;0.99124,MA0078.1;0.0642227,MA0081.1;0.527155,MA0083.1;1.7309,MA0084.1;0.58417,MA0087.1;0.522703,MA0088.1;0.000977565,MA0089.1;0,MA0090.1;0.232719,MA0091.1;0.361572,MA0092.1;0.490471,MA0093.1;1.00394,MA0095.1;0,MA0098.1;0,MA0100.1;0.350513,MA0101.1;0.106488,MA0103.1;0.473878,MA0105.1;0.00671316,MA0106.1;0.176444,MA0107.1;0.169146,MA0108.2;0.345418,MA0109.1;0,MA0111.1;0.0439819,MA0113.1;2.13809,MA0114.1;0.0135422,MA0115.1;0.365583,MA0116.1;0.0436546,MA0117.1;1.17644,MA0119.1;2.02749,MA0122.1;0.237097,MA0124.1;0.887885,MA0125.1;0.272745,MA0130.1;0,MA0131.1;0.0709376,MA0132.1;0,MA0133.1;0,MA0135.1;0.215386,MA0136.1;0.33922,MA0139.1;0.000350674,MA0140.1;0.26368,MA0141.1;0.0267885,MA0142.1;1.0705,MA0143.1;1.14732,MA0144.1;0.349813,MA0145.1;0.00446344,MA0146.1;1.955e-09,MA0147.1;0.300661,MA0148.1;0.212812,MA0149.1;0.0236308,MA0062.2;0.0902974,MA0035.2;0.788348,MA0039.2;5.77902e-09,MA0138.2;0.0646653,MA0002.2;0.127342,MA0137.2;0.239026,MA0104.2;0.149763,MA0047.2;0.165401,MA0112.2;2.73187e-05,MA0065.2;0.0391677,MA0150.1;0.104809,MA0151.1;0,MA0152.1;0.273429,MA0153.1;0.722842,MA0154.1;0.00234838,MA0155.1;0.0389398,MA0156.1;0.607111,MA0157.1;0.278642,MA0158.1;0,MA0159.1;0.00429051,MA0160.1;0.233502,MA0161.1;0,MA0162.1;1.26675e-06,MA0163.1;3.88148e-05,MA0164.1;0.204043,MA0080.2;0.339781,MA0018.2;0.177725,MA0099.2;1.60754,MA0079.2;0,MA0102.2;0.616902,MA0258.1;0.0594663,MA0259.1;0.110843,MA0442.1;0
}}
}}

Revision as of 18:46, 22 January 2013


Full id: C225_ductal_alveolar_giant_prostate_salivary_squamous_Tracheal



Phase1 CAGE Peaks

Hg19::chr10:16932413..16932437,-p@chr10:16932413..16932437
-
Hg19::chr10:17070392..17070407,-p@chr10:17070392..17070407
-
Hg19::chr10:4806777..4806787,-p@chr10:4806777..4806787
-
Hg19::chr10:4808676..4808703,-p@chr10:4808676..4808703
-
Hg19::chr10:4808737..4808750,-p@chr10:4808737..4808750
-
Hg19::chr11:13895146..13895156,+p@chr11:13895146..13895156
+
Hg19::chr12:76220619..76220626,-p@chr12:76220619..76220626
-
Hg19::chr13:63967430..63967434,+p@chr13:63967430..63967434
+
Hg19::chr15:35795980..35795985,-p@chr15:35795980..35795985
-
Hg19::chr15:35796430..35796456,-p@chr15:35796430..35796456
-
Hg19::chr17:66818826..66818835,+p@chr17:66818826..66818835
+
Hg19::chr18:2409216..2409225,-p@chr18:2409216..2409225
-
Hg19::chr1:162724324..162724330,+p@chr1:162724324..162724330
+
Hg19::chr1:162825560..162825574,-p1@C1orf110
Hg19::chr1:163063326..163063330,+p@chr1:163063326..163063330
+
Hg19::chr1:78001338..78001348,+p@chr1:78001338..78001348
+
Hg19::chr1:94240786..94240801,-p3@uc001dqd.1
Hg19::chr1:94240846..94240855,-p5@uc001dqd.1
Hg19::chr1:94240877..94240925,-p2@uc001dqd.1
Hg19::chr1:98779728..98779733,-p@chr1:98779728..98779733
-
Hg19::chr1:98850479..98850511,-p@chr1:98850479..98850511
-
Hg19::chr2:114004369..114004400,-p@chr2:114004369..114004400
-
Hg19::chr2:114004420..114004422,-p@chr2:114004420..114004422
-
Hg19::chr2:139757287..139757309,+p@chr2:139757287..139757309
+
Hg19::chr2:139791188..139791193,+p@chr2:139791188..139791193
+
Hg19::chr2:139791209..139791219,+p@chr2:139791209..139791219
+
Hg19::chr2:139791292..139791303,+p@chr2:139791292..139791303
+
Hg19::chr2:196278203..196278206,+p@chr2:196278203..196278206
+
Hg19::chr2:196278365..196278367,+p@chr2:196278365..196278367
+
Hg19::chr2:230450858..230450884,-p@chr2:230450858..230450884
-
Hg19::chr2:230450887..230450899,-p@chr2:230450887..230450899
-
Hg19::chr2:230680106..230680124,-p@chr2:230680106..230680124
-
Hg19::chr2:238378261..238378264,-p@chr2:238378261..238378264
-
Hg19::chr3:149051194..149051242,-p5@TM4SF18
Hg19::chr3:153599269..153599304,+p1@ENST00000463297
Hg19::chr3:188993877..188993894,+p@chr3:188993877..188993894
+
Hg19::chr3:189028187..189028196,+p@chr3:189028187..189028196
+
Hg19::chr3:189030852..189030859,+p@chr3:189030852..189030859
+
Hg19::chr3:189121193..189121200,+p@chr3:189121193..189121200
+
Hg19::chr3:189128229..189128239,+p@chr3:189128229..189128239
+
Hg19::chr3:189151408..189151415,+p@chr3:189151408..189151415
+
Hg19::chr3:83659759..83659783,-p@chr3:83659759..83659783
-
Hg19::chr3:84017708..84017724,+p@chr3:84017708..84017724
+
Hg19::chr4:125901946..125901955,+p@chr4:125901946..125901955
+
Hg19::chr4:81139190..81139200,-p@chr4:81139190..81139200
-
Hg19::chr4:81224883..81224888,+p@chr4:81224883..81224888
+
Hg19::chr5:141766141..141766182,+p@chr5:141766141..141766182
+
Hg19::chr5:27707663..27707672,+p@chr5:27707663..27707672
+
Hg19::chr5:27707697..27707707,+p@chr5:27707697..27707707
+
Hg19::chr5:56589068..56589074,-p@chr5:56589068..56589074
-
Hg19::chr5:56598008..56598013,-p@chr5:56598008..56598013
-
Hg19::chr5:57529651..57529657,+p@chr5:57529651..57529657
+
Hg19::chr5:57529696..57529706,+p@chr5:57529696..57529706
+
Hg19::chr5:57529719..57529726,+p@chr5:57529719..57529726
+
Hg19::chr5:92489155..92489169,-p@chr5:92489155..92489169
-
Hg19::chr6:145247788..145247818,-p@chr6:145247788..145247818
-
Hg19::chr6:165990105..165990115,-p10@PDE10A
Hg19::chr6:165990158..165990169,-p12@PDE10A
Hg19::chr6:169691363..169691375,-p@chr6:169691363..169691375
-
Hg19::chr8:41052616..41052617,-p@chr8:41052616..41052617
-
Hg19::chr8:41053290..41053297,-p@chr8:41053290..41053297
-
Hg19::chrX:13321104..13321106,-p@chrX:13321104..13321106
-
Hg19::chrX:18889509..18889513,+p@chrX:18889509..18889513
+


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:0019002GMP binding0.00809371024079062
GO:0030553cGMP binding0.00809371024079062
GO:0030551cyclic nucleotide binding0.0122606700313062
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0138255559698253
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0138255559698253
GO:0008081phosphoric diester hydrolase activity0.0337831481914176



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 pancreas3.10e-504
Uber Anatomy
Ontology termp-valuen
pancreas3.81e-2110
viscus1.85e-1218
Disease
Ontology termp-valuen
pancreas adenocarcinoma1.55e-982
pancreatic carcinoma1.55e-982
pancreatic ductal adenocarcinoma1.55e-982
pancreatic cancer3.10e-504
endocrine gland cancer4.27e-346


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)
MA0003.11.68077e-11
MA0004.10.59382
MA0006.10.0409568
MA0007.10.158809
MA0009.10.196219
MA0014.11.87231e-10
MA0017.10.0647838
MA0019.10.404253
MA0024.10.136013
MA0025.10.778709
MA0027.11.64023
MA0028.10.0150707
MA0029.10.146371
MA0030.10.433144
MA0031.10.349229
MA0038.10.934456
MA0040.10.149577
MA0041.12.22512
MA0042.13.51029
MA0043.10.57133
MA0046.10.189523
MA0048.10.0869886
MA0050.10.0625073
MA0051.10.136921
MA0052.10.462101
MA0055.10.000300352
MA0056.10
MA0057.10.000422302
MA0058.10.332561
MA0059.10.18173
MA0060.10.36689
MA0061.10.00911456
MA0063.10
MA0066.10.935977
MA0067.10.426099
MA0068.10.143048
MA0069.10.187175
MA0070.10.53276
MA0071.10.799731
MA0072.10.177746
MA0073.10.0292881
MA0074.10.13631
MA0076.10.0330734
MA0077.10.99124
MA0078.10.0642227
MA0081.10.527155
MA0083.11.7309
MA0084.10.58417
MA0087.10.522703
MA0088.10.000977565
MA0089.10
MA0090.10.232719
MA0091.10.361572
MA0092.10.490471
MA0093.11.00394
MA0095.10
MA0098.10
MA0100.10.350513
MA0101.10.106488
MA0103.10.473878
MA0105.10.00671316
MA0106.10.176444
MA0107.10.169146
MA0108.20.345418
MA0109.10
MA0111.10.0439819
MA0113.12.13809
MA0114.10.0135422
MA0115.10.365583
MA0116.10.0436546
MA0117.11.17644
MA0119.12.02749
MA0122.10.237097
MA0124.10.887885
MA0125.10.272745
MA0130.10
MA0131.10.0709376
MA0132.10
MA0133.10
MA0135.10.215386
MA0136.10.33922
MA0139.10.000350674
MA0140.10.26368
MA0141.10.0267885
MA0142.11.0705
MA0143.11.14732
MA0144.10.349813
MA0145.10.00446344
MA0146.11.955e-09
MA0147.10.300661
MA0148.10.212812
MA0149.10.0236308
MA0062.20.0902974
MA0035.20.788348
MA0039.25.77902e-09
MA0138.20.0646653
MA0002.20.127342
MA0137.20.239026
MA0104.20.149763
MA0047.20.165401
MA0112.22.73187e-05
MA0065.20.0391677
MA0150.10.104809
MA0151.10
MA0152.10.273429
MA0153.10.722842
MA0154.10.00234838
MA0155.10.0389398
MA0156.10.607111
MA0157.10.278642
MA0158.10
MA0159.10.00429051
MA0160.10.233502
MA0161.10
MA0162.11.26675e-06
MA0163.13.88148e-05
MA0164.10.204043
MA0080.20.339781
MA0018.20.177725
MA0099.21.60754
MA0079.20
MA0102.20.616902
MA0258.10.0594663
MA0259.10.110843
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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C225&oldid=2568736"