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{{Coexpression_clusters
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D3 (1,25-(OH)2D3) 24-hydroxylase activity!0.0016484163428706!1591$GO:0030303!stromelysin 2 activity!0.0016484163428706!4319$GO:0030574!collagen catabolic process!0.00689114531961418!4319$GO:0044256!protein digestion!0.00689114531961418!4319$GO:0044254!multicellular organismal protein catabolic process!0.00689114531961418!4319$GO:0044266!multicellular organismal macromolecule catabolic process!0.00689114531961418!4319$GO:0044259!multicellular organismal macromolecule metabolic process!0.00689114531961418!4319$GO:0044268!multicellular organismal protein metabolic process!0.00689114531961418!4319$GO:0032963!collagen metabolic process!0.00689114531961418!4319$GO:0044243!multicellular organismal catabolic process!0.00689114531961418!4319$GO:0044236!multicellular organismal metabolic 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5928,0.602504,0.815071,0.325254,0.81416,0.43333,0.388184,0.643716,0.598522,0.371702,0.788647,0.707691,0.68985|tfbs_overrepresentation_for_novel_motifs=0.157827,0.0953522,0.464859,2.04099,0.395738,0.25764,0.318839,0.215354,0.058273,0.00329214,0.234283,0.355038,0.3585,0.309388,0.124662,0.139688,0.511522,0.639388,0.689727,0.306606,0.152859,0.0268886,0.251588,0.12232,0.18461,0.374311,0.0323758,0.249905,0.127478,0.113679,0.217756,0.544857,0.260283,0.363901,0.340569,0.405974,0.102549,0.258546,1.04201,0.419472,0.690753,0.593399,0.0333136,0.781844,0.00483408,0.994428,0.319738,0.226038,0.18831,0.12756,0.386472,0.329494,0.625622,0.615394,0.758742,0.311792,0.130259,0.2852,0.113556,0.284391,0.582323,0.321692,0.0585016,0.48664,0.336598,0.456015,0.843028,1.20113,0.535417,1.04233,0.19602,1.26755,0.0158491,0.756844,0.150647,0.0336796,0.532449,0.471562,0.532468,0.532279,1.09095,0.48568,1.60321,0.477541,0.70821,0.00751148,0.0552506,0.49289,0.408949,1.29895,0.932961,0.68283,2.35858,0.270867,0.12599,0.60642,0.385004,0.599297,0.412954,0.020964,1.04735,0.555021,0.594155,1.28107,0.445845,0.230832,0.500571,0.826592,0.18443,0.115618,0.160439,0.591605,0.455599,0.677747,0.886618,0.333119,0.0385455,0.216858,0.453946,1.45742,0.748992,0.406842,0.255485,0.345739,0.993708,0.472239,0.313614,0.564749,0.78949,0.0864157,0.683478,0.219902,0.803201,0.908,0.945426,0.249246,0.611533,0.250344,0.904406,1.74999,1.35069,0.868456,0.315034,1.45285,1.13655,0.76278,0.432737,1.59165,0.203207,0.0770919,0.169169,0.00537053,0.683836,0.0546497,0.859679,1.07219,0.394947,0.116843,0.184652,0.164414,0.867287,0.66649,0.531753,0.499061,0.46162,0.335644,0.0708512,0.851721,0.0156497|tfbs_overrepresentation_jaspar=MA0003.1;0.114205,MA0004.1;0.238283,MA0006.1;0.392773,MA0007.1;0.223897,MA0009.1;0.644692,MA0014.1;0.024058,MA0017.1;0.89607,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.134741,MA0029.1;0.565022,MA0030.1;1.36515,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;0.70392,MA0042.1;0.646075,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.0172925,MA0050.1;1.20927,MA0051.1;0.851441,MA0052.1;0.574006,MA0055.1;0.0115209,MA0056.1;0,MA0057.1;0.189848,MA0058.1;0.167587,MA0059.1;0.166682,MA0060.1;0.212419,MA0061.1;1.08093,MA0063.1;0,MA0066.1;0.860141,MA0067.1;0.948938,MA0068.1;0.128042,MA0069.1;1.52585,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;0.616162,MA0073.1;0.72364,MA0074.1;0.316991,MA0076.1;0.178863,MA0077.1;0.608956,MA0078.1;1.039,MA0081.1;0.965129,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.0328284,MA0089.1;0,MA0090.1;0.554239,MA0091.1;0.240316,MA0092.1;1.14306,MA0093.1;0.12631,MA0095.1;0,MA0098.1;0,MA0100.1;0.332778,MA0101.1;1.89187,MA0103.1;0.118522,MA0105.1;0.554179,MA0106.1;0.93695,MA0107.1;1.0064,MA0108.2;1.23385,MA0109.1;0,MA0111.1;0.199239,MA0113.1;0.370073,MA0114.1;0.278245,MA0115.1;0.874839,MA0116.1;0.291279,MA0117.1;0.680135,MA0119.1;0.471628,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;0.327047,MA0139.1;1.01536,MA0140.1;0.7823,MA0141.1;0.165463,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.25687,MA0145.1;0.113672,MA0146.1;0.0055415,MA0147.1;0.0881384,MA0148.1;0.257816,MA0149.1;0.279141,MA0062.2;0.0439512,MA0035.2;0.780994,MA0039.2;0.0506563,MA0138.2;0.403517,MA0002.2;0.0530127,MA0137.2;0.430142,MA0104.2;0.0580852,MA0047.2;0.914023,MA0112.2;0.390337,MA0065.2;0.0080232,MA0150.1;0.5439,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;1.15225,MA0155.1;0.204406,MA0156.1;0.854962,MA0157.1;0.442323,MA0158.1;0,MA0159.1;0.0884959,MA0160.1;0.26995,MA0161.1;0,MA0162.1;0.0485277,MA0163.1;0.0267068,MA0164.1;0.99163,MA0080.2;0.397909,MA0018.2;0.357181,MA0099.2;0.292649,MA0079.2;0.055043,MA0102.2;1.16862,MA0258.1;0.520754,MA0259.1;0.0929051,MA0442.1;0}}
|full_id=C556_pharyngeal_Gingival_Retinal_lung_Mallassezderived_Small_mesothelioma
|gostat_on_coexpression_clusters=GO:0030342!1-alpha,25-dihydroxyvitamin D3 (1,25-(OH)2D3) 24-hydroxylase activity!0.0016484163428706!1591$GO:0030303!stromelysin 2 activity!0.0016484163428706!4319$GO:0030574!collagen catabolic process!0.00689114531961418!4319$GO:0044256!protein digestion!0.00689114531961418!4319$GO:0044254!multicellular organismal protein catabolic process!0.00689114531961418!4319$GO:0044266!multicellular organismal macromolecule catabolic process!0.00689114531961418!4319$GO:0044259!multicellular organismal macromolecule metabolic process!0.00689114531961418!4319$GO:0044268!multicellular organismal protein metabolic process!0.00689114531961418!4319$GO:0032963!collagen metabolic process!0.00689114531961418!4319$GO:0044243!multicellular organismal catabolic process!0.00689114531961418!4319$GO:0044236!multicellular organismal metabolic process!0.00689114531961418!4319$GO:0007586!digestion!0.0260638153203052!4319
|id=C556
}}

Latest revision as of 11:25, 17 September 2013


Full id: C556_pharyngeal_Gingival_Retinal_lung_Mallassezderived_Small_mesothelioma



Phase1 CAGE Peaks

Hg19::chr11:102642814..102642823,-p@chr11:102642814..102642823
-
Hg19::chr11:102651279..102651288,-p2@MMP10
Hg19::chr11:102651343..102651365,-p1@MMP10
Hg19::chr11:102700844..102700849,-p@chr11:102700844..102700849
-
Hg19::chr14:22659199..22659211,-p@chr14:22659199..22659211
-
Hg19::chr14:22677969..22677976,-p@chr14:22677969..22677976
-
Hg19::chr14:22678054..22678089,-p@chr14:22678054..22678089
-
Hg19::chr14:22678115..22678119,-p@chr14:22678115..22678119
-
Hg19::chr16:23119386..23119416,-p@chr16:23119386..23119416
-
Hg19::chr1:211565263..211565280,+p@chr1:211565263..211565280
+
Hg19::chr20:52771475..52771478,-p@chr20:52771475..52771478
-
Hg19::chr20:52790360..52790374,-p2@CYP24A1
Hg19::chr20:52790516..52790531,-p1@CYP24A1
Hg19::chr20:52790691..52790695,-p5@CYP24A1
Hg19::chr5:170179543..170179549,+p@chr5:170179543..170179549
+
Hg19::chr8:61167556..61167596,-p@chr8:61167556..61167596
-


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:00303421-alpha,25-dihydroxyvitamin D3 (1,25-(OH)2D3) 24-hydroxylase activity0.0016484163428706
GO:0030303stromelysin 2 activity0.0016484163428706
GO:0030574collagen catabolic process0.00689114531961418
GO:0044256protein digestion0.00689114531961418
GO:0044254multicellular organismal protein catabolic process0.00689114531961418
GO:0044266multicellular organismal macromolecule catabolic process0.00689114531961418
GO:0044259multicellular organismal macromolecule metabolic process0.00689114531961418
GO:0044268multicellular organismal protein metabolic process0.00689114531961418
GO:0032963collagen metabolic process0.00689114531961418
GO:0044243multicellular organismal catabolic process0.00689114531961418
GO:0044236multicellular organismal metabolic process0.00689114531961418
GO:0007586digestion0.0260638153203052



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 prostate2.59e-123
endo-epithelial cell7.58e-0842
epithelial cell of uterus8.02e-076
stromal cell of endometrium8.02e-076
Uber Anatomy
Ontology termp-valuen
tonsil7.06e-341
mucosa-associated lymphoid tissue7.06e-341
lymphoid tissue7.06e-341
tonsillar ring7.06e-341
open tracheal system trachea6.48e-182
pharynx4.80e-1311
Disease
Ontology termp-valuen
female reproductive endometrioid cancer8.02e-076


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)
MA0003.10.114205
MA0004.10.238283
MA0006.10.392773
MA0007.10.223897
MA0009.10.644692
MA0014.10.024058
MA0017.10.89607
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.11.36515
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.70392
MA0042.10.646075
MA0043.10.644989
MA0046.10.634468
MA0048.10.0172925
MA0050.11.20927
MA0051.10.851441
MA0052.10.574006
MA0055.10.0115209
MA0056.10
MA0057.10.189848
MA0058.10.167587
MA0059.10.166682
MA0060.10.212419
MA0061.11.08093
MA0063.10
MA0066.10.860141
MA0067.10.948938
MA0068.10.128042
MA0069.11.52585
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.72364
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.11.039
MA0081.10.965129
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.0328284
MA0089.10
MA0090.10.554239
MA0091.10.240316
MA0092.11.14306
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.11.89187
MA0103.10.118522
MA0105.10.554179
MA0106.10.93695
MA0107.11.0064
MA0108.21.23385
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.10.278245
MA0115.10.874839
MA0116.10.291279
MA0117.10.680135
MA0119.10.471628
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.11.01536
MA0140.10.7823
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.25687
MA0145.10.113672
MA0146.10.0055415
MA0147.10.0881384
MA0148.10.257816
MA0149.10.279141
MA0062.20.0439512
MA0035.20.780994
MA0039.20.0506563
MA0138.20.403517
MA0002.20.0530127
MA0137.20.430142
MA0104.20.0580852
MA0047.20.914023
MA0112.20.390337
MA0065.20.0080232
MA0150.10.5439
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.11.15225
MA0155.10.204406
MA0156.10.854962
MA0157.10.442323
MA0158.10
MA0159.10.0884959
MA0160.10.26995
MA0161.10
MA0162.10.0485277
MA0163.10.0267068
MA0164.10.99163
MA0080.20.397909
MA0018.20.357181
MA0099.20.292649
MA0079.20.055043
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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