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Coexpression cluster:C587: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.237220288771276

Latest revision as of 11:26, 17 September 2013


Full id: C587_Osteoblast_Monocytederived_CD14_Macrophage_leiomyoma_Adipocyte_Dendritic



Phase1 CAGE Peaks

Hg19::chr11:1774396..1774410,-p@chr11:1774396..1774410
-
Hg19::chr11:1774555..1774567,-p@chr11:1774555..1774567
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Hg19::chr11:1774591..1774602,-p@chr11:1774591..1774602
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Hg19::chr11:1774626..1774637,-p@chr11:1774626..1774637
-
Hg19::chr11:1774653..1774680,-p@chr11:1774653..1774680
-
Hg19::chr11:1774731..1774765,-p@chr11:1774731..1774765
-
Hg19::chr11:1778628..1778664,-p3@CTSD
Hg19::chr11:1780775..1780793,-p2@ENST00000427721
Hg19::chr11:1780825..1780859,-p@chr11:1780825..1780859
-
Hg19::chr11:1782587..1782602,-p@chr11:1782587..1782602
-
Hg19::chr17:42429493..42429515,+p@chr17:42429493..42429515
+
Hg19::chr19:40872708..40872743,+p8@PLD3
Hg19::chr19:49469548..49469569,+p@chr19:49469548..49469569
+
Hg19::chr2:85628961..85628975,-p10@CAPG
Hg19::chr7:97911681..97911696,+p@chr7:97911681..97911696
+


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:0048770pigment granule0.000962696371097009
GO:0042470melanosome0.000962696371097009
GO:0004192cathepsin D activity0.00320852466737313
GO:0016023cytoplasmic membrane-bound vesicle0.00695351994664752
GO:0031988membrane-bound vesicle0.00695351994664752
GO:0031410cytoplasmic vesicle0.00721811799281055
GO:0031982vesicle0.00721811799281055
GO:0004630phospholipase D activity0.00721811799281055
GO:0008290F-actin capping protein complex0.0158032041510128
GO:0051693actin filament capping0.0158032041510128
GO:0051016barbed-end actin filament capping0.0158032041510128
GO:0030835negative regulation of actin filament depolymerization0.0158032041510128
GO:0030834regulation of actin filament depolymerization0.0158032041510128
GO:0030042actin filament depolymerization0.0158032041510128
GO:0004194pepsin A activity0.0166720528007639
GO:0044444cytoplasmic part0.0168152519673891
GO:0008064regulation of actin polymerization and/or depolymerization0.0215137929918326
GO:0051261protein depolymerization0.0215137929918326
GO:0030832regulation of actin filament length0.0215137929918326
GO:0032535regulation of cellular component size0.0215137929918326
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0215137929918326
GO:0030031cell projection biogenesis0.0215263959366968
GO:0051129negative regulation of cellular component organization and biogenesis0.0215263959366968
GO:0051493regulation of cytoskeleton organization and biogenesis0.0215263959366968
GO:0033043regulation of organelle organization and biogenesis0.0215263959366968
GO:0008154actin polymerization and/or depolymerization0.0225432140480013
GO:0004190aspartic-type endopeptidase activity0.0302278645094982
GO:0051128regulation of cellular component organization and biogenesis0.0342769630157552
GO:0051248negative regulation of protein metabolic process0.0344147421805016
GO:0004620phospholipase activity0.0375507630894644
GO:0005737cytoplasm0.0375507630894644
GO:0008081phosphoric diester hydrolase activity0.04095819083259
GO:0016298lipase activity0.04095819083259
GO:0016042lipid catabolic process0.0411571714271229
GO:0004091carboxylesterase activity0.0464739618400419
GO:0043231intracellular membrane-bound organelle0.0464739618400419
GO:0043227membrane-bound organelle0.0464739618400419
GO:0005764lysosome0.0464739618400419
GO:0000323lytic vacuole0.0464739618400419
GO:0032990cell part morphogenesis0.0464739618400419
GO:0030030cell projection organization and biogenesis0.0464739618400419
GO:0048858cell projection morphogenesis0.0464739618400419



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
mesoderm8.10e-14315
mesoderm-derived structure8.10e-14315
presumptive mesoderm8.10e-14315
bone marrow1.95e-1376
multi-cellular organism1.22e-12656
bone element2.00e-1282
skeletal element2.19e-1290
immune system5.83e-1293
skeletal system2.14e-11100
musculoskeletal system2.00e-10167
anatomical system2.18e-09624
anatomical group3.08e-09625
hemolymphoid system4.87e-09108
organ6.01e-09503
hematopoietic system2.19e-0898
blood island2.19e-0898
germ layer4.71e-08560
germ layer / neural crest4.71e-08560
embryonic tissue4.71e-08560
presumptive structure4.71e-08560
germ layer / neural crest derived structure4.71e-08560
epiblast (generic)4.71e-08560
embryonic structure1.18e-07564
lateral plate mesoderm1.80e-07203
developing anatomical structure5.82e-07581
embryo5.83e-07592


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)
MA0003.11.15038
MA0004.10.256222
MA0006.10.137644
MA0007.11.25763
MA0009.10.669377
MA0014.10.142864
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.441458
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.229721
MA0056.10
MA0057.10.688135
MA0058.10.538866
MA0059.10.182001
MA0060.10.0671843
MA0061.15.54703
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.0373092
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.18.31188
MA0074.10.894848
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.12.0778
MA0089.10
MA0090.10.205547
MA0091.10.716673
MA0092.10.228476
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.437519
MA0103.11.91714
MA0105.11.29048
MA0106.10.37688
MA0107.11.08326
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.11.57072
MA0115.10.900969
MA0116.13.57057
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.71772
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.284854
MA0145.10.478485
MA0146.11.33403
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.0512998
MA0035.20.305721
MA0039.20.530814
MA0138.20.425279
MA0002.21.75425
MA0137.20.153033
MA0104.20.0667907
MA0047.20.366327
MA0112.21.33111
MA0065.21.06382
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.11.26909
MA0155.12.06149
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.671959
MA0160.10.288813
MA0161.10
MA0162.12.33131
MA0163.10.765815
MA0164.11.03839
MA0080.20.139746
MA0018.20.378086
MA0099.20.312108
MA0079.20.949531
MA0102.21.1957
MA0258.10.27007
MA0259.10.340204
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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