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Coexpression cluster:C429: Difference between revisions

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{{Coexpression_clusters
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organism during symbiotic interaction!0.00996864124799369!83737$GO:0009057!macromolecule catabolic process!0.00996864124799369!83737;84750$GO:0009605!response to external stimulus!0.00996864124799369!83737;84750$GO:0006004!fucose metabolic process!0.0121373491035594!84750$GO:0008417!fucosyltransferase activity!0.0137966119781209!84750$GO:0044248!cellular catabolic process!0.0137966119781209!83737;84750$GO:0051701!interaction with host!0.0152552373701995!83737$GO:0009056!catabolic process!0.0180874098061372!83737;84750$GO:0044403!symbiosis, encompassing mutualism through parasitism!0.0194100405888146!83737$GO:0044419!interspecies interaction between organisms!0.0194100405888146!83737$GO:0006950!response to stress!0.0249860686985649!83737;84750$GO:0019058!viral infectious cycle!0.0279804151465854!83737$GO:0022415!viral reproductive 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94162,0.902349,0.837997,0.796905,0.60471,0.800383,0.477957,0.546935,0.398458,0.630918,0.397101,0.571333,0.409122,0.455611,0.652345,0.587818,0.29239,0.412154,0.513129,0.249504,0.670969,0.826744,0.932004,0.924988,0.837437,0.327135,0.903795,0.193916,0.510403,0.861772,0.933906,0.893703,0.77679,0.922501,0.905043,0.661494,0.738866,0.829802,0.817952,0.925149,0.6122,0.803083,0.610814,0.848285,0.578241,0.608998,0.810398,0.803076,0.720199,0.922142,0.88976,0.74821,0.579411,0.529166,0.952316,0.85937,0.832337,0.53824,0.497829,0.335185,0.76404,0.382429,0.911627,0.431946,0.6957,0.19714,0.854845,0.773167,0.730683,0.555577,0.892922,0.829334,0.967895|tfbs_overrepresentation_for_novel_motifs=0.086801,0.123941,0.283006,2.91518,1.79318,0.164151,0.21518,0.246499,0.0978594,0.0364691,0.446032,1.2761,0.0638208,0.596995,0.847482,0.546223,0.386278,0.374077,0.189125,0.11553,0.0832107,1.17512,0.159229,0.834629,0.106647,0.263074,0.48237,0.157865,0.0653771,0.115495,0.412868,0.416977,0.0319501,0.172492,0.0500279,0.0130697,0.72396,0.16489,0.157401,0.082891,0.185583,0.388602,0.381667,0.225216,0.0834249,0.0986693,0.617815,0.138738,0.117154,0.065433,0.752093,0.224271,0.290248,1.21241,0.61862,0.209199,0.238182,0.186863,0.115345,0.18619,0.451758,0.217609,0.0982927,0.953606,0.230363,0.892008,0.699678,1.04962,0.408258,0.893579,0.11533,1.13172,0.951109,0.616804,0.0606565,0.0522785,0.257418,0.349828,0.405538,0.689568,0.633422,0.362659,0.651143,0.251709,0.570388,0.0650075,0.014259,0.0379885,0.293613,1.14619,0.786844,0.546282,1.10147,0.137237,1.29175,0.0384041,0.186686,0.467605,0.297172,0.00541109,0.65113,0.426385,0.462798,1.01029,0.871551,0.863684,0.376249,0.204779,0.106511,0.209231,0.298191,0.460417,0.275626,0.460536,0.741849,0.181704,0.0927767,0.411067,0.333893,0.0350599,0.60929,0.79308,0.162396,0.238235,1.97142,0.350442,0.210743,0.435409,0.648109,0.350382,0.546896,1.33889,0.66129,0.235825,0.798972,0.86769,0.128702,0.478286,1.79241,1.59408,1.19737,0.724259,1.14509,0.464565,0.327989,1.0238,0.314828,1.43649,0.120862,0.574568,0.41217,0.351137,0.547236,0.227594,0.217268,0.922839,0.281215,0.211649,0.106679,0.30612,0.723128,0.530809,1.84129,0.0932398,0.340824,0.649817,0.029532,0.214247,0.133367|tfbs_overrepresentation_jaspar=MA0003.1;0.175839,MA0004.1;0.454064,MA0006.1;0.845891,MA0007.1;0.137043,MA0009.1;0.510226,MA0014.1;0.0358715,MA0017.1;0.27776,MA0019.1;0.250001,MA0024.1;0.419164,MA0025.1;0.630648,MA0027.1;2.07466,MA0028.1;0.247069,MA0029.1;0.435662,MA0030.1;0.425859,MA0031.1;0.371592,MA0038.1;0.21714,MA0040.1;0.440685,MA0041.1;0.160207,MA0042.1;0.140252,MA0043.1;0.510506,MA0046.1;0.500598,MA0048.1;0.0737273,MA0050.1;0.856183,MA0051.1;1.1536,MA0052.1;0.444013,MA0055.1;0.0197225,MA0056.1;0,MA0057.1;0.021569,MA0058.1;0.645288,MA0059.1;0.0932742,MA0060.1;0.242587,MA0061.1;0.625508,MA0063.1;0,MA0066.1;1.16636,MA0067.1;0.802392,MA0068.1;0.0481509,MA0069.1;1.24347,MA0070.1;0.487346,MA0071.1;0.190167,MA0072.1;0.483399,MA0073.1;0.000913068,MA0074.1;0.213609,MA0076.1;0.334977,MA0077.1;2.0834,MA0078.1;1.42963,MA0081.1;0.0933581,MA0083.1;0.516887,MA0084.1;0.981601,MA0087.1;0.481255,MA0088.1;0.377487,MA0089.1;0,MA0090.1;0.721145,MA0091.1;0.15013,MA0092.1;1.29707,MA0093.1;0.856503,MA0095.1;0,MA0098.1;0,MA0100.1;0.227084,MA0101.1;0.868045,MA0103.1;0.469617,MA0105.1;0.128351,MA0106.1;0.690773,MA0107.1;0.617546,MA0108.2;0.369058,MA0109.1;0,MA0111.1;0.375752,MA0113.1;0.259368,MA0114.1;0.331605,MA0115.1;0.730438,MA0116.1;0.0385791,MA0117.1;0.543727,MA0119.1;0.0851434,MA0122.1;0.567011,MA0124.1;0.691722,MA0125.1;0.614264,MA0130.1;0,MA0131.1;0.302006,MA0132.1;0,MA0133.1;0,MA0135.1;0.537249,MA0136.1;0.222179,MA0139.1;0.0657272,MA0140.1;0.188358,MA0141.1;0.637815,MA0142.1;0.345512,MA0143.1;0.259501,MA0144.1;0.0312488,MA0145.1;0.436464,MA0146.1;0.549621,MA0147.1;0.998135,MA0148.1;0.4933,MA0149.1;0.18183,MA0062.2;0.603241,MA0035.2;0.18788,MA0039.2;0.00114874,MA0138.2;0.288795,MA0002.2;1.8397,MA0137.2;0.073361,MA0104.2;0.4561,MA0047.2;0.238164,MA0112.2;0.144552,MA0065.2;0.0334139,MA0150.1;0.10696,MA0151.1;0,MA0152.1;0.192836,MA0153.1;0.598889,MA0154.1;0.00259032,MA0155.1;0.0627913,MA0156.1;0.0744198,MA0157.1;0.323429,MA0158.1;0,MA0159.1;0.0399934,MA0160.1;0.99551,MA0161.1;0,MA0162.1;0.137435,MA0163.1;0.0404314,MA0164.1;0.740687,MA0080.2;0.230472,MA0018.2;0.248141,MA0099.2;1.68742,MA0079.2;0.00162827,MA0102.2;1.01759,MA0258.1;0.283423,MA0259.1;0.374822,MA0442.1;0}}
|full_id=C429_anaplastic_Mast_clear_Neutrophils_squamous_Eosinophils_oral
|id=C429
}}

Latest revision as of 11:22, 17 September 2013


Full id: C429_anaplastic_Mast_clear_Neutrophils_squamous_Eosinophils_oral



Phase1 CAGE Peaks

Hg19::chr10:28367018..28367027,+p@chr10:28367018..28367027
+
Hg19::chr10:28367095..28367106,+p@chr10:28367095..28367106
+
Hg19::chr10:28367218..28367230,+p@chr10:28367218..28367230
+
Hg19::chr10:28367236..28367266,+p@chr10:28367236..28367266
+
Hg19::chr10:28367270..28367278,+p@chr10:28367270..28367278
+
Hg19::chr12:127256858..127256871,-p1@ENST00000542248
Hg19::chr16:56648492..56648498,-p@chr16:56648492..56648498
-
Hg19::chr16:56648503..56648510,-p@chr16:56648503..56648510
-
Hg19::chr16:56648532..56648539,-p@chr16:56648532..56648539
-
Hg19::chr17:31099607..31099657,-p@chr17:31099607..31099657
-
Hg19::chr20:32951056..32951067,+p2@ITCH
Hg19::chr20:32951070..32951122,+p1@ITCH
Hg19::chr21:19858196..19858204,-p2@TMPRSS15
Hg19::chr2:17603261..17603273,-p@chr2:17603261..17603273
-
Hg19::chr2:26915639..26915654,+p3@KCNK3
Hg19::chr4:20253897..20253905,+p@chr4:20253897..20253905
+
Hg19::chr8:33330595..33330689,-p1@FUT10
Hg19::chr8:33370607..33370676,-p1@TTI2
Hg19::chr8:33744758..33744766,-p@chr8:33744758..33744766
-
Hg19::chr8:33744817..33744827,-p@chr8:33744817..33744827
-
Hg19::chr8:55467072..55467091,+p1@ENST00000518787
Hg19::chr9:106503385..106503391,-p@chr9:106503385..106503391
-
Hg19::chr9:114714967..114714986,-p@chr9:114714967..114714986
-


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:0022414reproductive process0.00996864124799369
GO:0009611response to wounding0.00996864124799369
GO:0046920alpha(1,3)-fucosyltransferase activity0.00996864124799369
GO:0044265cellular macromolecule catabolic process0.00996864124799369
GO:0019317fucose catabolic process0.00996864124799369
GO:0042355L-fucose catabolic process0.00996864124799369
GO:0044409entry into host0.00996864124799369
GO:0030260entry into host cell0.00996864124799369
GO:0042354L-fucose metabolic process0.00996864124799369
GO:0019059initiation of viral infection0.00996864124799369
GO:0052192movement in environment of other organism during symbiotic interaction0.00996864124799369
GO:0046718entry of virus into host cell0.00996864124799369
GO:0052126movement in host environment0.00996864124799369
GO:0051828entry into other organism during symbiotic interaction0.00996864124799369
GO:0051806entry into cell of other organism during symbiotic interaction0.00996864124799369
GO:0009057macromolecule catabolic process0.00996864124799369
GO:0009605response to external stimulus0.00996864124799369
GO:0006004fucose metabolic process0.0121373491035594
GO:0008417fucosyltransferase activity0.0137966119781209
GO:0044248cellular catabolic process0.0137966119781209
GO:0051701interaction with host0.0152552373701995
GO:0009056catabolic process0.0180874098061372
GO:0044403symbiosis, encompassing mutualism through parasitism0.0194100405888146
GO:0044419interspecies interaction between organisms0.0194100405888146
GO:0006950response to stress0.0249860686985649
GO:0019058viral infectious cycle0.0279804151465854
GO:0022415viral reproductive process0.0301318038301384
GO:0009566fertilization0.0301318038301384



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 cervix1.44e-092
bone matrix secreting cell2.02e-092
osteocyte2.02e-092
osteoclast2.02e-092


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)
MA0003.10.175839
MA0004.10.454064
MA0006.10.845891
MA0007.10.137043
MA0009.10.510226
MA0014.10.0358715
MA0017.10.27776
MA0019.10.250001
MA0024.10.419164
MA0025.10.630648
MA0027.12.07466
MA0028.10.247069
MA0029.10.435662
MA0030.10.425859
MA0031.10.371592
MA0038.10.21714
MA0040.10.440685
MA0041.10.160207
MA0042.10.140252
MA0043.10.510506
MA0046.10.500598
MA0048.10.0737273
MA0050.10.856183
MA0051.11.1536
MA0052.10.444013
MA0055.10.0197225
MA0056.10
MA0057.10.021569
MA0058.10.645288
MA0059.10.0932742
MA0060.10.242587
MA0061.10.625508
MA0063.10
MA0066.11.16636
MA0067.10.802392
MA0068.10.0481509
MA0069.11.24347
MA0070.10.487346
MA0071.10.190167
MA0072.10.483399
MA0073.10.000913068
MA0074.10.213609
MA0076.10.334977
MA0077.12.0834
MA0078.11.42963
MA0081.10.0933581
MA0083.10.516887
MA0084.10.981601
MA0087.10.481255
MA0088.10.377487
MA0089.10
MA0090.10.721145
MA0091.10.15013
MA0092.11.29707
MA0093.10.856503
MA0095.10
MA0098.10
MA0100.10.227084
MA0101.10.868045
MA0103.10.469617
MA0105.10.128351
MA0106.10.690773
MA0107.10.617546
MA0108.20.369058
MA0109.10
MA0111.10.375752
MA0113.10.259368
MA0114.10.331605
MA0115.10.730438
MA0116.10.0385791
MA0117.10.543727
MA0119.10.0851434
MA0122.10.567011
MA0124.10.691722
MA0125.10.614264
MA0130.10
MA0131.10.302006
MA0132.10
MA0133.10
MA0135.10.537249
MA0136.10.222179
MA0139.10.0657272
MA0140.10.188358
MA0141.10.637815
MA0142.10.345512
MA0143.10.259501
MA0144.10.0312488
MA0145.10.436464
MA0146.10.549621
MA0147.10.998135
MA0148.10.4933
MA0149.10.18183
MA0062.20.603241
MA0035.20.18788
MA0039.20.00114874
MA0138.20.288795
MA0002.21.8397
MA0137.20.073361
MA0104.20.4561
MA0047.20.238164
MA0112.20.144552
MA0065.20.0334139
MA0150.10.10696
MA0151.10
MA0152.10.192836
MA0153.10.598889
MA0154.10.00259032
MA0155.10.0627913
MA0156.10.0744198
MA0157.10.323429
MA0158.10
MA0159.10.0399934
MA0160.10.99551
MA0161.10
MA0162.10.137435
MA0163.10.0404314
MA0164.10.740687
MA0080.20.230472
MA0018.20.248141
MA0099.21.68742
MA0079.20.00162827
MA0102.21.01759
MA0258.10.283423
MA0259.10.374822
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
BATF#1053844.236139442139760.01344575848030930.0475006450605496
ESR1#209956.688826803511840.0007460539146123150.00587477379086146



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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