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

Latest revision as of 11:43, 17 September 2013


Full id: C1356_CD14_thymus_Hodgkin_NK_anaplastic_hepatoblastoma_lymphangiectasia



Phase1 CAGE Peaks

Hg19::chr12:123717458..123717464,+p2@C12orf65
Hg19::chr12:58241001..58241005,+p@chr12:58241001..58241005
+
Hg19::chr14:99947613..99947617,-p8@SETD3
Hg19::chr19:56116608..56116632,-p@chr19:56116608..56116632
-
Hg19::chr1:147071419..147071423,-p@chr1:147071419..147071423
-
Hg19::chr4:100871681..100871699,+p1@ENST00000501976


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:0008079translation termination factor activity0.00739694285085992
GO:0006415translational termination0.00739694285085992
GO:0003747translation release factor activity0.00739694285085992
GO:0043624cellular protein complex disassembly0.00796417945172759
GO:0043241protein complex disassembly0.00796417945172759
GO:0032984macromolecular complex disassembly0.00796417945172759
GO:0022411cellular component disassembly0.0119425752711976
GO:0008135translation factor activity, nucleic acid binding0.0427693486322997



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
bone element2.86e-0982
bone marrow6.61e-0976
hematopoietic system9.85e-0998
blood island9.85e-0998
immune system7.35e-0893
skeletal element3.96e-0790
hemolymphoid system9.42e-07108
Disease
Ontology termp-valuen
cancer8.47e-18235
disease of cellular proliferation1.44e-16239
cell type cancer6.03e-12143
carcinoma3.30e-11106
hematologic cancer2.02e-0851
immune system cancer2.02e-0851
organ system cancer2.12e-07137


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)
MA0003.10.321379
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.12.04333
MA0058.10.458909
MA0059.10.457555
MA0060.12.90543
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.18.00296
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.13.94689
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.441872
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.24.88217
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.11.09123
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.11.60684
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.25.61874
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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
BCL3#602211.51570093457940.01162725346801640.0424757327974452
BHLHE40#8553214.95727118232580.00701655948451940.029638117533012
CCNT2#90555.280167980802190.0005100943974832530.0044666511929868
CHD2#110646.896015222744570.001115391320135990.00765980760676503
EGR1#195854.156815912341780.001617966818864440.0101306256951669
GTF2B#2959210.64794331144140.01351345865760110.0477236705353264
HEY1#2346253.366759202588090.004423827045203030.0209475912574338
HMGN3#932445.452365148900390.002729616882333770.0149852006714706
IRF1#365956.364303127969920.000205667514205090.00243893601862898
IRF3#3661215.66065073716320.006417620989932530.0279131233786258
NFYA#480039.212790349915260.002822755564364270.0154494166432575
NFYB#480138.379896626768230.003703996878629040.0186825910367593
PAX5#507944.446377020785220.005874733519240790.0263598253143147
POLR2A#543062.147453176558070.01019570676818780.038003833797165
POU2F2#545246.070749371828350.001815326209524520.0108928959492405
RDBP#7936251.21280133000830.0006240180493507170.00513730262148349
SIN3A#2594243.605923151210090.01273893844487140.0459390902332074
SP1#666765.69838137814092.91961319085282e-050.000609112029643384
TAF1#687263.343046285745290.0007162474284635620.00572773087146294
TAF7#687947.622046269949280.000759279015141480.00596586977598262
TBP#690863.706770687096390.000385416472907960.0037756787368947
ZBTB7A#5134144.901272871917260.004079628118843750.0194829338837589



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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