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{{Coexpression_clusters
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superoxide dismutase activity!0.0027375485694101!6648$GO:0001315!age-dependent response to reactive oxygen species!0.0027375485694101!6648$GO:0000303!response to superoxide!0.00342193571176262!6648$GO:0000305!response to oxygen radical!0.00342193571176262!6648$GO:0016721!oxidoreductase activity, acting on superoxide radicals as acceptor!0.00410632285411515!6648$GO:0004784!superoxide dismutase activity!0.00410632285411515!6648$GO:0001836!release of cytochrome c from mitochondria!0.00508401877176161!6648$GO:0008637!apoptotic mitochondrial changes!0.00574885199576121!6648$GO:0042542!response to hydrogen peroxide!0.00574885199576121!6648$GO:0006801!superoxide metabolic process!0.00574885199576121!6648$GO:0000302!response to reactive oxygen species!0.00671943739764298!6648$GO:0006302!double-strand break repair!0.0082126457082303!6648$GO:0006800!oxygen and reactive oxygen species metabolic process!0.00947612966334266!6648$GO:0008632!apoptotic program!0.0162427881784999!6648$GO:0007005!mitochondrion organization and biogenesis!0.0162427881784999!6648$GO:0006979!response to oxidative stress!0.0205316142705758!6648$GO:0030145!manganese ion binding!0.0236717435119579!6648$GO:0031980!mitochondrial lumen!0.0263669151685289!6648$GO:0005759!mitochondrial matrix!0.0263669151685289!6648$GO:0043066!negative regulation of apoptosis!0.0299826748078249!6648$GO:0043069!negative regulation of programmed cell death!0.0299826748078249!6648$GO:0005743!mitochondrial inner membrane!0.0389478501011528!6648$GO:0019866!organelle inner membrane!0.0393968946293367!6648$GO:0006281!DNA repair!0.0438007771105616!6648$GO:0031966!mitochondrial membrane!0.0438007771105616!6648$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0438007771105616!6648$GO:0005740!mitochondrial envelope!0.0438007771105616!6648$GO:0006974!response to DNA damage stimulus!0.0438007771105616!6648$GO:0009719!response to endogenous stimulus!0.0486675301228462!6648$GO:0042981!regulation of apoptosis!0.0486675301228462!6648$GO:0043067!regulation of programmed cell death!0.0486675301228462!6648$GO:0044429!mitochondrial part!0.0486675301228462!6648$GO:0042221!response to chemical stimulus!0.0486675301228462!6648$GO:0031967!organelle envelope!0.0486675301228462!6648$GO:0031975!envelope!0.0486675301228462!6648$GO:0006366!transcription from RNA polymerase II 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|full_id=C954_heart_CD14_Neutrophils_Eosinophils_Lymphatic_renal_Monocytederived
|gostat_on_coexpression_clusters=GO:0008383!manganese superoxide dismutase activity!0.0027375485694101!6648$GO:0001315!age-dependent response to reactive oxygen species!0.0027375485694101!6648$GO:0000303!response to superoxide!0.00342193571176262!6648$GO:0000305!response to oxygen radical!0.00342193571176262!6648$GO:0016721!oxidoreductase activity, acting on superoxide radicals as acceptor!0.00410632285411515!6648$GO:0004784!superoxide dismutase activity!0.00410632285411515!6648$GO:0001836!release of cytochrome c from mitochondria!0.00508401877176161!6648$GO:0008637!apoptotic mitochondrial changes!0.00574885199576121!6648$GO:0042542!response to hydrogen peroxide!0.00574885199576121!6648$GO:0006801!superoxide metabolic process!0.00574885199576121!6648$GO:0000302!response to reactive oxygen species!0.00671943739764298!6648$GO:0006302!double-strand break repair!0.0082126457082303!6648$GO:0006800!oxygen and reactive oxygen species metabolic process!0.00947612966334266!6648$GO:0008632!apoptotic program!0.0162427881784999!6648$GO:0007005!mitochondrion organization and biogenesis!0.0162427881784999!6648$GO:0006979!response to oxidative stress!0.0205316142705758!6648$GO:0030145!manganese ion binding!0.0236717435119579!6648$GO:0031980!mitochondrial lumen!0.0263669151685289!6648$GO:0005759!mitochondrial matrix!0.0263669151685289!6648$GO:0043066!negative regulation of apoptosis!0.0299826748078249!6648$GO:0043069!negative regulation of programmed cell death!0.0299826748078249!6648$GO:0005743!mitochondrial inner membrane!0.0389478501011528!6648$GO:0019866!organelle inner membrane!0.0393968946293367!6648$GO:0006281!DNA repair!0.0438007771105616!6648$GO:0031966!mitochondrial membrane!0.0438007771105616!6648$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0438007771105616!6648$GO:0005740!mitochondrial envelope!0.0438007771105616!6648$GO:0006974!response to DNA damage stimulus!0.0438007771105616!6648$GO:0009719!response to endogenous stimulus!0.0486675301228462!6648$GO:0042981!regulation of apoptosis!0.0486675301228462!6648$GO:0043067!regulation of programmed cell death!0.0486675301228462!6648$GO:0044429!mitochondrial part!0.0486675301228462!6648$GO:0042221!response to chemical stimulus!0.0486675301228462!6648$GO:0031967!organelle envelope!0.0486675301228462!6648$GO:0031975!envelope!0.0486675301228462!6648$GO:0006366!transcription from RNA polymerase II promoter!0.0486675301228462!6648
|id=C954
}}

Latest revision as of 11:34, 17 September 2013


Full id: C954_heart_CD14_Neutrophils_Eosinophils_Lymphatic_renal_Monocytederived



Phase1 CAGE Peaks

Hg19::chr6:160100686..160100698,-p4@AK093984
Hg19::chr6:160101581..160101593,-p18@SOD2
Hg19::chr6:160101609..160101626,-p21@SOD2
Hg19::chr6:160101648..160101695,-p7@SOD2
Hg19::chr6:160102006..160102195,-p1@BC041951
Hg19::chr6:160102208..160102232,-p6@BC041951
Hg19::chr6:160102300..160102326,-p5@BC041951
Hg19::chr6:160102610..160102627,-p3@BC041951
Hg19::chr6:160112805..160112821,-p@chr6:160112805..160112821
-


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:0008383manganese superoxide dismutase activity0.0027375485694101
GO:0001315age-dependent response to reactive oxygen species0.0027375485694101
GO:0000303response to superoxide0.00342193571176262
GO:0000305response to oxygen radical0.00342193571176262
GO:0016721oxidoreductase activity, acting on superoxide radicals as acceptor0.00410632285411515
GO:0004784superoxide dismutase activity0.00410632285411515
GO:0001836release of cytochrome c from mitochondria0.00508401877176161
GO:0008637apoptotic mitochondrial changes0.00574885199576121
GO:0042542response to hydrogen peroxide0.00574885199576121
GO:0006801superoxide metabolic process0.00574885199576121
GO:0000302response to reactive oxygen species0.00671943739764298
GO:0006302double-strand break repair0.0082126457082303
GO:0006800oxygen and reactive oxygen species metabolic process0.00947612966334266
GO:0008632apoptotic program0.0162427881784999
GO:0007005mitochondrion organization and biogenesis0.0162427881784999
GO:0006979response to oxidative stress0.0205316142705758
GO:0030145manganese ion binding0.0236717435119579
GO:0031980mitochondrial lumen0.0263669151685289
GO:0005759mitochondrial matrix0.0263669151685289
GO:0043066negative regulation of apoptosis0.0299826748078249
GO:0043069negative regulation of programmed cell death0.0299826748078249
GO:0005743mitochondrial inner membrane0.0389478501011528
GO:0019866organelle inner membrane0.0393968946293367
GO:0006281DNA repair0.0438007771105616
GO:0031966mitochondrial membrane0.0438007771105616
GO:0006357regulation of transcription from RNA polymerase II promoter0.0438007771105616
GO:0005740mitochondrial envelope0.0438007771105616
GO:0006974response to DNA damage stimulus0.0438007771105616
GO:0009719response to endogenous stimulus0.0486675301228462
GO:0042981regulation of apoptosis0.0486675301228462
GO:0043067regulation of programmed cell death0.0486675301228462
GO:0044429mitochondrial part0.0486675301228462
GO:0042221response to chemical stimulus0.0486675301228462
GO:0031967organelle envelope0.0486675301228462
GO:0031975envelope0.0486675301228462
GO:0006366transcription from RNA polymerase II promoter0.0486675301228462



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><br>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.10e-16108
hematopoietic system1.67e-1698
blood island1.67e-1698
bone marrow1.12e-1576
immune system9.75e-1493
bone element2.57e-1382
musculoskeletal system3.46e-13167
skeletal element4.48e-1390
skeletal system4.55e-13100
adult organism8.53e-13114
mesoderm6.34e-09315
mesoderm-derived structure6.34e-09315
presumptive mesoderm6.34e-09315
lateral plate mesoderm4.56e-08203
anatomical system6.22e-07624
germ layer6.25e-07560
germ layer / neural crest6.25e-07560
embryonic tissue6.25e-07560
presumptive structure6.25e-07560
germ layer / neural crest derived structure6.25e-07560
epiblast (generic)6.25e-07560
anatomical group7.67e-07625


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)
MA0003.10.000472949
MA0004.11.06719
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.10.815464
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.11.04113
MA0051.10.510444
MA0052.10.795605
MA0055.10.0199484
MA0056.10
MA0057.10.0725989
MA0058.11.56347
MA0059.10.865474
MA0060.10.488252
MA0061.10.851955
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.13.08738
MA0072.11.96038
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.11.94461
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.11.95538
MA0088.10.0408613
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.11.76221
MA0093.10.73976
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.746654
MA0103.11.31682
MA0105.10.854766
MA0106.10.554855
MA0107.11.75554
MA0108.21.68573
MA0109.10
MA0111.11.70852
MA0113.11.39997
MA0114.10.582067
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.83188
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.0045741
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.23.07257
MA0039.20.00489248
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.21.34084
MA0112.20.0433683
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.11.20819
MA0153.10.969315
MA0154.10.225151
MA0155.10.359913
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.21.36887
MA0099.20.481058
MA0079.23.47892e-06
MA0102.21.41188
MA0258.10.180288
MA0259.10.624802
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

No analysis results for this cluster

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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