Personal tools

Coexpression cluster:C194

From FANTOM5_SSTAR

Revision as of 13:44, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C194_MCF7_breast_prostate_Intestinal_diffuse_Wilms_Alveolar



Phase1 CAGE Peaks

Hg19::chr10:109305043..109305046,+p@chr10:109305043..109305046
+
Hg19::chr10:118030368..118030379,+p@chr10:118030368..118030379
+
Hg19::chr10:8091813..8091823,+p@chr10:8091813..8091823
+
Hg19::chr10:8093055..8093080,-p@chr10:8093055..8093080
-
Hg19::chr10:8093191..8093214,+p1@ENST00000418270
Hg19::chr10:8093226..8093237,+p2@ENST00000418270
Hg19::chr10:8094059..8094066,+p@chr10:8094059..8094066
+
Hg19::chr10:8095431..8095449,-p1@FLJ45983
Hg19::chr10:8096323..8096329,-p@chr10:8096323..8096329
-
Hg19::chr10:8100452..8100463,+p20@GATA3
Hg19::chr10:8910201..8910211,+p@chr10:8910201..8910211
+
Hg19::chr11:72493920..72493932,-p19@STARD10
Hg19::chr11:9113106..9113118,-p3@SCUBE2
Hg19::chr11:9113137..9113151,-p1@SCUBE2
Hg19::chr12:3324464..3324485,+p4@TSPAN9
Hg19::chr12:53297486..53297500,-p15@KRT8
Hg19::chr12:53359307..53359335,+p@chr12:53359307..53359335
+
Hg19::chr13:24289325..24289337,+p@chr13:24289325..24289337
+
Hg19::chr14:100438174..100438181,+p28@EVL
Hg19::chr14:100625961..100625988,-p1@DEGS2
Hg19::chr14:105267423..105267443,+p2@ZBTB42
Hg19::chr14:38064198..38064200,-p11@FOXA1
Hg19::chr14:38064307..38064323,-p3@FOXA1
Hg19::chr14:38064429..38064486,-p1@FOXA1
Hg19::chr14:38065203..38065215,-p9@FOXA1
Hg19::chr15:99194008..99194023,-p@chr15:99194008..99194023
-
Hg19::chr15:99395486..99395494,-p@chr15:99395486..99395494
-
Hg19::chr16:68271763..68271795,+p@chr16:68271763..68271795
+
Hg19::chr16:68386079..68386100,+p4@PRMT7
Hg19::chr16:78085184..78085211,+p@chr16:78085184..78085211
+
Hg19::chr17:4542343..4542380,+p@chr17:4542343..4542380
+
Hg19::chr17:57914914..57914926,+p6@AK310806
Hg19::chr17:57970074..57970117,-p2@TUBD1
Hg19::chr17:58677539..58677610,+p1@PPM1D
Hg19::chr17:58677652..58677698,+p2@PPM1D
Hg19::chr17:59469536..59469541,+p@chr17:59469536..59469541
+
Hg19::chr17:61523756..61523792,+p@chr17:61523756..61523792
+
Hg19::chr17:73521554..73521574,-p@chr17:73521554..73521574
-
Hg19::chr17:74574500..74574512,-p@chr17:74574500..74574512
-
Hg19::chr19:14183628..14183639,+p3@LOC113230
Hg19::chr1:109792128..109792139,+p@chr1:109792128..109792139
+
Hg19::chr1:150953891..150953894,+p@chr1:150953891..150953894
+
Hg19::chr1:96504230..96504238,-p@chr1:96504230..96504238
-
Hg19::chr20:19738569..19738582,-p2@LOC100287166
Hg19::chr20:45986315..45986328,-p@chr20:45986315..45986328
-
Hg19::chr20:46414348..46414364,+p@chr20:46414348..46414364
+
Hg19::chr20:46414380..46414395,+p@chr20:46414380..46414395
+
Hg19::chr20:49347516..49347535,-p@chr20:49347516..49347535
-
Hg19::chr20:49347538..49347547,-p@chr20:49347538..49347547
-
Hg19::chr20:49347901..49347919,+p4@PARD6B
Hg19::chr20:49411523..49411535,+p4@BCAS4
Hg19::chr20:49411543..49411635,+p1@BCAS4
Hg19::chr20:52210553..52210568,-p7@ZNF217
Hg19::chr20:52482691..52482707,-p@chr20:52482691..52482707
-
Hg19::chr20:55204118..55204122,-p@chr20:55204118..55204122
-
Hg19::chr21:41711178..41711186,-p@chr21:41711178..41711186
-
Hg19::chr2:11679963..11679986,+p8@GREB1
Hg19::chr2:11682790..11682822,+p4@GREB1
Hg19::chr2:189470761..189470766,-p@chr2:189470761..189470766
-
Hg19::chr2:227660810..227660851,-p@chr2:227660810..227660851
-
Hg19::chr2:227661562..227661575,-p@chr2:227661562..227661575
-
Hg19::chr2:227661576..227661601,-p@chr2:227661576..227661601
-
Hg19::chr2:227662026..227662050,-p@chr2:227662026..227662050
-
Hg19::chr2:227662613..227662634,+p@chr2:227662613..227662634
+
Hg19::chr2:227662666..227662677,+p@chr2:227662666..227662677
+
Hg19::chr2:75136085..75136090,+p@chr2:75136085..75136090
+
Hg19::chr3:161089270..161089273,-p3@SPTSSB
Hg19::chr3:161089297..161089312,-p1@SPTSSB
Hg19::chr3:161089631..161089635,+p@chr3:161089631..161089635
+
Hg19::chr5:116790756..116790798,+p2@ENST00000504107
Hg19::chr5:116790848..116790851,+p4@ENST00000504107
Hg19::chr5:179740905..179740933,+p@chr5:179740905..179740933
+
Hg19::chr6:26272822..26272838,-p3@HIST1H2APS4
Hg19::chr7:156518511..156518549,-p5@LMBR1
Hg19::chr7:80551671..80551680,-p38@SEMA3C
Hg19::chr8:100905448..100905460,-p10@COX6C
Hg19::chr8:91871372..91871381,-p1@ENST00000517884
Hg19::chr8:91871468..91871473,-p2@ENST00000517884
Hg19::chr8:91871545..91871568,-p3@ENST00000517884
Hg19::chr9:131940726..131940731,+p@chr9:131940726..131940731
+
Hg19::chr9:134420902..134420915,+p@chr9:134420902..134420915
+
Hg19::chr9:136739422..136739457,+p@chr9:136739422..136739457
+
Hg19::chr9:137249109..137249127,+p@chr9:137249109..137249127
+
Hg19::chr9:91150087..91150100,+p1@NXNL2
Hg19::chrX:139586386..139586401,-p@chrX:139586386..139586401
-
Hg19::chrX:139586415..139586427,-p@chrX:139586415..139586427
-
Hg19::chrX:71960688..71960693,-p1@ENST00000364401


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:0016277[myelin basic protein]-arginine N-methyltransferase activity0.0467473959727593
GO:0042415norepinephrine metabolic process0.0467473959727593
GO:0042421norepinephrine biosynthetic process0.0467473959727593
GO:0035243protein-arginine omega-N symmetric methyltransferase activity0.0467473959727593
GO:0007275multicellular organismal development0.0467473959727593
GO:0042445hormone metabolic process0.0467473959727593
GO:0048485sympathetic nervous system development0.0467473959727593
GO:0035241protein-arginine omega-N monomethyltransferase activity0.0467473959727593



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><br>uberon_data<br>disease_data<br>

Disease
Ontology termp-valuen
thoracic cancer5.37e-544
breast cancer5.37e-544
disease of anatomical entity1.29e-0839


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
BHLHE40#855363.094607830826030.01331902595812510.0470831895491681
E2F1#1869512.876745401825816.95797147555338e-151.21518993801893e-12
EP300#2033282.180119176255743.32779437008602e-050.00066124717697377
ESR1#209993.182958961671150.002106743222986970.0121796930786347
FOXA1#3169303.821179223926024.93171208322702e-115.56223626630828e-09
FOXA2#3170143.963522902727741.08014361323558e-050.000280062360533046
GATA3#2625165.009014502474671.06378187758549e-076.21366417858784e-06
HDAC2#3066152.313037971832110.001860601225738130.0109753929067983
HNF4G#317482.643992875995110.01092635257248610.0402148765265674
MYC#4609392.341022907962844.27933857225565e-082.81264846537324e-06
POLR2A#5430671.653785779648176.53632711446568e-095.14041767701567e-07
SUZ12#2351274.032304211234950.001823529155677530.0109139003719087



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:C194&oldid=2556525"