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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 10:53, 17 September 2013


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)
MA0003.15.24372
MA0004.10.482271
MA0006.10.844949
MA0007.10.426863
MA0009.10.123344
MA0014.18.00878
MA0017.10.0988179
MA0019.10.0195011
MA0024.10.563692
MA0025.10.197015
MA0027.11.50196
MA0028.10.238402
MA0029.10.0849308
MA0030.10.579045
MA0031.10.457702
MA0038.10.0619426
MA0040.10.0873223
MA0041.10.0285972
MA0042.10.0200198
MA0043.10.123499
MA0046.11.80409
MA0048.12.34454
MA0050.10.14606
MA0051.10.0598711
MA0052.10.298798
MA0055.15.72614
MA0056.10
MA0057.10.198798
MA0058.10.130791
MA0059.10.230212
MA0060.11.40884
MA0061.10.0319129
MA0063.10
MA0066.10.329204
MA0067.10.321182
MA0068.13.29551
MA0069.10.116197
MA0070.10.110912
MA0071.10.124821
MA0072.10.352222
MA0073.17.10165
MA0074.10.539065
MA0076.10.153651
MA0077.10.105288
MA0078.10.287175
MA0081.10.0620248
MA0083.10.399708
MA0084.10.467465
MA0087.10.107695
MA0088.10.849714
MA0089.10
MA0090.10.470032
MA0091.11.00123
MA0092.10.380567
MA0093.10.653486
MA0095.10
MA0098.10
MA0100.12.0824
MA0101.10.215169
MA0103.11.26713
MA0105.10.942663
MA0106.10.213747
MA0107.10.2217
MA0108.20.20559
MA0109.10
MA0111.11.6291
MA0113.10.446129
MA0114.10.308575
MA0115.10.736328
MA0116.10.477413
MA0117.10.142504
MA0119.11.78163
MA0122.10.473907
MA0124.10.671777
MA0125.10.186249
MA0130.10
MA0131.10.133596
MA0132.10
MA0133.10
MA0135.11.36883
MA0136.10.0654996
MA0139.11.57796
MA0140.11.31654
MA0141.10.12667
MA0142.10.0473337
MA0143.10.235303
MA0144.10.0121521
MA0145.11.76085
MA0146.12.73001
MA0147.11.31137
MA0148.10.197037
MA0149.10.0397429
MA0062.20.0133717
MA0035.20.253105
MA0039.28.07272
MA0138.20.288975
MA0002.20.683808
MA0137.20.0360313
MA0104.20.960933
MA0047.20.385808
MA0112.24.60514
MA0065.21.26884
MA0150.10.0332706
MA0151.10
MA0152.10.128574
MA0153.11.00406
MA0154.11.23123
MA0155.10.704615
MA0156.10.0372444
MA0157.10.356776
MA0158.10
MA0159.11.3178
MA0160.10.103371
MA0161.10
MA0162.110.5413
MA0163.13.56308
MA0164.10.102678
MA0080.20.00899355
MA0018.20.413908
MA0099.20.0462878
MA0079.214.5418
MA0102.20.498347
MA0258.11.6831
MA0259.10.71488
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
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

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