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Coexpression cluster:C199: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;9:6.80063859101148:7.49081057670852e-06:0.000214455253788613!SETDB1#9869;7:3.40048413549486:0.00462445111234762:0.0218401487619822!SIRT6#51548;4:7.40426043325421:0.00218328487869065:0.0125929248050794!SUZ12#23512;12:7.24565507147897:1.02249555920046e-07:5.98925483496003e-06
|tf_chipseq_enrich=CTBP2#1488;9:6.80063859101148:7.49081057670852e-06:0.000214455253788613!SETDB1#9869;7:3.40048413549486:0.00462445111234762:0.0218401487619822!SIRT6#51548;4:7.40426043325421:0.00218328487869065:0.0125929248050794!SUZ12#23512;12:7.24565507147897:1.02249555920046e-07:5.98925483496003e-06
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|tfbs_overrepresentation_for_novel_motifs=0.236238,2.09371e-05,0.0221374,0.621318,0.532538,0.0361119,0.0694715,0.723786,0.0752658,0.000501965,0.323194,0.235282,0.000135724,0.168299,0.365262,0.181233,0.244932,0.206586,0.637967,0.000706259,0.731483,0.0111694,0.374426,0.227655,0.0401449,0.266266,0.0168474,0.369331,0.000357963,0.159059,0.671523,0.0836645,0.00627477,0.0314993,0.389216,0.000146833,0.0176973,0.893457,0.114656,0.00148875,0.725385,0.0554567,0.00617629,0.233002,4.30888e-05,0.289552,1.24767,0.715443,0.755519,0.147698,0.529485,0.382483,0.0604793,0.11739,1.73077,0.570327,0.154921,0.279952,0.0101944,0.733312,0.678226,0.363611,0.128104,0.0600154,0.975703,0.727221,0.25777,0.543298,0.57512,0.409608,0.0481122,0.00322804,0.432265,0.199649,0.0265092,0.231495,0.000685063,0.200814,1.43716,0.311218,0.395082,2.88899,1.76959,1.14858,0.975654,1.30992e-06,13.7845,0.0340127,0.325588,0.629621,0.864932,0.154359,1.05152,0.0446857,0.000339668,0.0560964,1.17713,0.353292,0.142939,0.000670111,0.2979,0.61762,0.106678,0.906803,0.39345,0.077288,0.0653136,0.164475,0.0116384,0.00861255,0.244601,0.699184,0.938991,0.0876693,0.289088,0.523502,0.0154378,0.447714,0.0484986,0.658547,1.07724,2.29214,0.386308,0.422803,0.370678,0.201531,0.174098,0.639032,0.22103,0.106595,0.154735,0.152429,0.651466,0.216634,0.333134,0.0801541,0.26467,1.15697,0.81675,1.05119,0.676239,0.275894,0.581551,0.107613,0.0463475,0.128504,0.0417269,0.899965,0.0163716,0.222985,0.00117532,0.000956455,0.154943,0.0341233,0.0152838,0.434031,0.301069,0.862819,0.00177778,0.00108892,0.275052,0.145005,0.0779994,0.0292089,2.12874,1.34294,0.117238,0.179844,2.17663e-09
}}
}}

Revision as of 13:45, 26 November 2012


Full id: C199_glioblastoma_B_osteosarcoma_Fibroblast_heart_rhabdomyosarcoma_myxofibrosarcoma



Phase1 CAGE Peaks

Hg19::chr10:28030013..28030015,+p@chr10:28030013..28030015
+
Hg19::chr10:28033530..28033552,-p@chr10:28033530..28033552
-
Hg19::chr10:28033565..28033575,-p@chr10:28033565..28033575
-
Hg19::chr10:28033579..28033592,-p@chr10:28033579..28033592
-
Hg19::chr10:28033614..28033628,-p@chr10:28033614..28033628
-
Hg19::chr10:28033640..28033643,-p@chr10:28033640..28033643
-
Hg19::chr10:28033659..28033673,+p3@ENST00000419777
Hg19::chr10:28033753..28033766,+p4@ENST00000419777
Hg19::chr10:28033776..28033788,+p1@ENST00000419777
Hg19::chr10:28033806..28033813,+p5@ENST00000419777
Hg19::chr10:28033817..28033825,+p2@ENST00000419777
Hg19::chr10:28034395..28034404,-p9@MKX
Hg19::chr10:28034450..28034462,+p@chr10:28034450..28034462
+
Hg19::chr10:28035746..28035751,-p@chr10:28035746..28035751
-
Hg19::chr10:28287942..28287952,-p8@ARMC4
Hg19::chr10:28287968..28288010,-p1@ARMC4
Hg19::chr10:28367310..28367318,+p@chr10:28367310..28367318
+
Hg19::chr10:28414812..28414824,-p@chr10:28414812..28414824
-
Hg19::chr10:28488010..28488022,-p@chr10:28488010..28488022
-
Hg19::chr10:28491892..28491902,-p7@MPP7
Hg19::chr10:28506871..28506903,-p@chr10:28506871..28506903
-
Hg19::chr10:28506967..28506974,-p@chr10:28506967..28506974
-
Hg19::chr10:28507002..28507009,-p@chr10:28507002..28507009
-
Hg19::chr10:28509539..28509568,-p@chr10:28509539..28509568
-
Hg19::chr10:28509632..28509637,-p@chr10:28509632..28509637
-
Hg19::chr10:28509658..28509676,-p@chr10:28509658..28509676
-
Hg19::chr10:28509721..28509724,-p@chr10:28509721..28509724
-
Hg19::chr10:28527477..28527523,+p@chr10:28527477..28527523
+
Hg19::chr10:28527860..28527872,-p9@MPP7
Hg19::chr10:28530804..28530813,-p@chr10:28530804..28530813
-
Hg19::chr10:28530831..28530841,-p@chr10:28530831..28530841
-
Hg19::chr10:54329319..54329326,-p@chr10:54329319..54329326
-
Hg19::chr10:54329365..54329373,-p@chr10:54329365..54329373
-
Hg19::chr10:54329394..54329397,-p@chr10:54329394..54329397
-
Hg19::chr10:54329422..54329434,-p@chr10:54329422..54329434
-
Hg19::chr10:54329447..54329454,-p@chr10:54329447..54329454
-
Hg19::chr10:54373438..54373447,-p@chr10:54373438..54373447
-
Hg19::chr10:54399928..54399940,+p@chr10:54399928..54399940
+
Hg19::chr10:54399943..54399963,+p@chr10:54399943..54399963
+
Hg19::chr15:36045989..36046028,+p@chr15:36045989..36046028
+
Hg19::chr18:38446239..38446249,-p@chr18:38446239..38446249
-
Hg19::chr18:38529517..38529528,+p@chr18:38529517..38529528
+
Hg19::chr18:38529571..38529575,+p@chr18:38529571..38529575
+
Hg19::chr18:39041105..39041117,-p@chr18:39041105..39041117
-
Hg19::chr18:70417486..70417495,-p@chr18:70417486..70417495
-
Hg19::chr18:70417532..70417548,-p@chr18:70417532..70417548
-
Hg19::chr18:70417551..70417561,-p@chr18:70417551..70417561
-
Hg19::chr18:70417646..70417651,-p@chr18:70417646..70417651
-
Hg19::chr18:70417659..70417666,-p@chr18:70417659..70417666
-
Hg19::chr18:70423377..70423388,-p@chr18:70423377..70423388
-
Hg19::chr1:170043617..170043675,-p2@KIFAP3
Hg19::chr1:170043681..170043695,-p3@KIFAP3
Hg19::chr1:170043917..170043928,-p4@KIFAP3
Hg19::chr1:198636194..198636203,-p4@ENST00000413577
Hg19::chr1:70541774..70541784,+p@chr1:70541774..70541784
+
Hg19::chr21:26714477..26714509,+p@chr21:26714477..26714509
+
Hg19::chr21:26714551..26714589,+p@chr21:26714551..26714589
+
Hg19::chr2:70025987..70025999,-p5@ENST00000502349
p5@uc002sft.1
Hg19::chr2:70026040..70026056,-p4@ENST00000502349
p4@uc002sft.1
Hg19::chr2:70026073..70026084,-p3@ENST00000502349
p3@uc002sft.1
Hg19::chr3:30166734..30166774,+p@chr3:30166734..30166774
+
Hg19::chr3:30274017..30274027,-p@chr3:30274017..30274027
-
Hg19::chr3:30274089..30274100,-p@chr3:30274089..30274100
-
Hg19::chr4:176708533..176708544,-p28@GPM6A
Hg19::chr4:176729849..176729872,+p@chr4:176729849..176729872
+
Hg19::chr4:176734130..176734137,-p33@GPM6A
Hg19::chr4:176749234..176749238,+p@chr4:176749234..176749238
+
Hg19::chr4:176749383..176749408,+p@chr4:176749383..176749408
+
Hg19::chr5:103227130..103227137,-p@chr5:103227130..103227137
-
Hg19::chr5:103227146..103227159,-p@chr5:103227146..103227159
-
Hg19::chr5:103248950..103248994,+p@chr5:103248950..103248994
+
Hg19::chr5:103251049..103251059,+p@chr5:103251049..103251059
+
Hg19::chr5:169014305..169014309,+p8@CCDC99
Hg19::chr5:169122140..169122157,+p3@DOCK2
Hg19::chr5:169122159..169122169,+p5@DOCK2
Hg19::chr5:24160807..24160831,-p@chr5:24160807..24160831
-
Hg19::chr5:24163239..24163250,-p@chr5:24163239..24163250
-
Hg19::chr5:24170343..24170359,+p3@ENST00000514047
Hg19::chr6:113010123..113010128,-p@chr6:113010123..113010128
-
Hg19::chr6:73270707..73270718,-p@chr6:73270707..73270718
-
Hg19::chr9:106443940..106443941,+p@chr9:106443940..106443941
+
Hg19::chrY:18192344..18192349,+p@chrY:18192344..18192349
+
Hg19::chrY:3781821..3781829,-p@chrY:3781821..3781829
-


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:0016939kinesin II complex0.019604380077711
GO:0042608T cell receptor binding0.0261334029735661
GO:0048247lymphocyte chemotaxis0.0261334029735661
GO:0030676Rac guanyl-nucleotide exchange factor activity0.0342925194531488
GO:0019894kinesin binding0.03526711454817



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>

Uber Anatomy
Ontology termp-valuen
brain6.59e-0768
future brain6.59e-0768
Disease
Ontology termp-valuen
nervous system cancer5.98e-3411


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)

{{{tfbs_overrepresentation_jaspar}}}



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
CTBP2#148896.800638591011487.49081057670852e-060.000214455253788613
SETDB1#986973.400484135494860.004624451112347620.0218401487619822
SIRT6#5154847.404260433254210.002183284878690650.0125929248050794
SUZ12#23512127.245655071478971.02249555920046e-075.98925483496003e-06



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

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