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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:09, 17 September 2013


Full id: C266_acute_chronic_leukemia_small_choriocarcinoma_hepatoma_Mast



Phase1 CAGE Peaks

Hg19::chr10:126826943..126826984,-p28@CTBP2
Hg19::chr10:127505042..127505063,-p8@UROS
Hg19::chr10:25820836..25820845,+p@chr10:25820836..25820845
+
Hg19::chr10:25820884..25820895,+p@chr10:25820884..25820895
+
Hg19::chr10:25820904..25820913,+p@chr10:25820904..25820913
+
Hg19::chr10:25821044..25821091,+p@chr10:25821044..25821091
+
Hg19::chr11:33914678..33914683,-p@chr11:33914678..33914683
-
Hg19::chr11:74807933..74807937,-p@chr11:74807933..74807937
-
Hg19::chr12:115758751..115758760,-p@chr12:115758751..115758760
-
Hg19::chr12:115758858..115758876,-p@chr12:115758858..115758876
-
Hg19::chr12:115758891..115758908,-p@chr12:115758891..115758908
-
Hg19::chr12:71617078..71617086,-p@chr12:71617078..71617086
-
Hg19::chr12:78870953..78870955,+p@chr12:78870953..78870955
+
Hg19::chr14:105166013..105166017,+p@chr14:105166013..105166017
+
Hg19::chr14:67859531..67859537,-p9@PLEK2
Hg19::chr16:24124312..24124336,+p@chr16:24124312..24124336
+
Hg19::chr16:24127820..24127835,-p@chr16:24127820..24127835
-
Hg19::chr16:88558406..88558427,+p@chr16:88558406..88558427
+
Hg19::chr16:88858526..88858538,-p@chr16:88858526..88858538
-
Hg19::chr17:25899255..25899265,+p@chr17:25899255..25899265
+
Hg19::chr17:72864739..72864767,-p5@FDXR
Hg19::chr18:31319109..31319114,+p9@ASXL3
Hg19::chr18:43620002..43620017,-p@chr18:43620002..43620017
-
Hg19::chr19:51105300..51105305,+p@chr19:51105300..51105305
+
Hg19::chr19:5131212..5131221,+p4@KDM4B
Hg19::chr19:5131887..5131896,+p@chr19:5131887..5131896
+
Hg19::chr19:59067834..59067852,-p@chr19:59067834..59067852
-
Hg19::chr1:159253361..159253368,+p@chr1:159253361..159253368
+
Hg19::chr1:176849256..176849268,+p@chr1:176849256..176849268
+
Hg19::chr1:179011968..179011976,-p@chr1:179011968..179011976
-
Hg19::chr22:36007795..36007820,-p@chr22:36007795..36007820
-
Hg19::chr2:219258788..219258830,+p@chr2:219258788..219258830
+
Hg19::chr2:220386017..220386029,+p@chr2:220386017..220386029
+
Hg19::chr2:225249514..225249517,-p@chr2:225249514..225249517
-
Hg19::chr2:5211564..5211614,+p@chr2:5211564..5211614
+
Hg19::chr3:139059704..139059754,-p@chr3:139059704..139059754
-
Hg19::chr3:50211282..50211296,+p@chr3:50211282..50211296
+
Hg19::chr3:52334122..52334129,-p@chr3:52334122..52334129
-
Hg19::chr3:52334165..52334173,-p@chr3:52334165..52334173
-
Hg19::chr4:124087446..124087458,+p@chr4:124087446..124087458
+
Hg19::chr4:134160987..134160994,-p@chr4:134160987..134160994
-
Hg19::chr4:171901111..171901116,+p@chr4:171901111..171901116
+
Hg19::chr5:1201575..1201595,+p3@SLC6A19
Hg19::chr5:1201599..1201625,+p2@SLC6A19
Hg19::chr6:31615512..31615544,-p@chr6:31615512..31615544
-
Hg19::chr6:42072634..42072643,-p13@C6orf132
Hg19::chrX:11327532..11327554,-p@chrX:11327532..11327554
-
Hg19::chrX:48559008..48559045,-p@chrX:48559008..48559045
-
Hg19::chrX:48650688..48650735,+p5@GATA1


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:0016730oxidoreductase activity, acting on iron-sulfur proteins as donors0.00715294948781349
GO:0004324ferredoxin-NADP+ reductase activity0.00715294948781349
GO:0008937ferredoxin reductase activity0.00715294948781349
GO:0016731oxidoreductase activity, acting on iron-sulfur proteins as donors, NAD or NADP as acceptor0.00715294948781349
GO:0046502uroporphyrinogen III metabolic process0.00953656411554144
GO:0006780uroporphyrinogen III biosynthetic process0.00953656411554144
GO:0004852uroporphyrinogen-III synthase activity0.0163459895047015
GO:0015804neutral amino acid transport0.0485828177802072
GO:0006783heme biosynthetic process0.0485828177802072
GO:0015175neutral amino acid transmembrane transporter activity0.0485828177802072



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><br>disease_data<br>

Disease
Ontology termp-valuen
myeloid leukemia7.41e-0831


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)
MA0003.10.111394
MA0004.10.0321488
MA0006.10.00619213
MA0007.10.516216
MA0009.10.263756
MA0014.19.83564e-05
MA0017.10.487315
MA0019.10.0819566
MA0024.10.193834
MA0025.10.3631
MA0027.11.74826
MA0028.10.239827
MA0029.11.12232
MA0030.10.198787
MA0031.10.15963
MA0038.10.228762
MA0040.10.209871
MA0041.10.0369855
MA0042.10.0289066
MA0043.10.263979
MA0046.10.256123
MA0048.10.0627077
MA0050.10.0291141
MA0051.10.224229
MA0052.10.609377
MA0055.10.101147
MA0056.10
MA0057.10.162473
MA0058.10.0134788
MA0059.10.013294
MA0060.10.720202
MA0061.10.392691
MA0063.10
MA0066.12.36099
MA0067.10.514146
MA0068.10.151529
MA0069.10.253439
MA0070.11.27393
MA0071.13.31611
MA0072.11.26233
MA0073.10.00846835
MA0074.10.223426
MA0076.10.919936
MA0077.10.6681
MA0078.10.340465
MA0081.10.0634322
MA0083.10.269067
MA0084.10.679402
MA0087.10.240948
MA0088.10.181032
MA0089.10
MA0090.10.0824972
MA0091.10.0328063
MA0092.10.103168
MA0093.10.00645236
MA0095.10
MA0098.10
MA0100.10.522734
MA0101.10.104492
MA0103.10.195176
MA0105.10.0397821
MA0106.10.0803211
MA0107.10.109939
MA0108.20.477395
MA0109.10
MA0111.10.228735
MA0113.10.0873401
MA0114.10.0126519
MA0115.10.449785
MA0116.10.368435
MA0117.10.290704
MA0119.11.46638
MA0122.10.833799
MA0124.10.415762
MA0125.10.349207
MA0130.10
MA0131.10.113217
MA0132.10
MA0133.10
MA0135.11.42091
MA0136.10.236422
MA0139.10.495226
MA0140.13.9567
MA0141.18.90482
MA0142.10.860025
MA0143.10.613856
MA0144.10.0871497
MA0145.10.060301
MA0146.10.0447471
MA0147.10.0152484
MA0148.10.350475
MA0149.12.60366
MA0062.20.240243
MA0035.23.94993
MA0039.20.00770712
MA0138.20.342023
MA0002.21.41774
MA0137.20.00830828
MA0104.20.0055454
MA0047.20.261058
MA0112.21.65992
MA0065.20.16838
MA0150.10.644059
MA0151.10
MA0152.10.1926
MA0153.10.336269
MA0154.10.853625
MA0155.10.176093
MA0156.10.256234
MA0157.10.39953
MA0158.10
MA0159.12.1494
MA0160.11.04202
MA0161.10
MA0162.10.015859
MA0163.10.0853647
MA0164.10.309505
MA0080.20.871864
MA0018.20.581793
MA0099.21.15075
MA0079.23.17066e-05
MA0102.20.713248
MA0258.12.12315
MA0259.10.0559863
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
GATA1#2623133.597632772845023.96023418025606e-050.000738576602771004
GATA2#2624123.121207771482610.0003188913615455430.00326452606434571
STAT2#677345.327654790729850.006739339895501240.0286432230230844
TAL1#6886127.314763267944545.70523040920804e-083.56795544136095e-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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