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Coexpression cluster:C478: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:23, 17 September 2013


Full id: C478_blood_Whole_Reticulocytes_liver_skeletal_lung_Neutrophils



Phase1 CAGE Peaks

Hg19::chr11:5247855..5247868,+p1@DQ655984
Hg19::chr11:5247857..5247902,-p2@HBB
Hg19::chr11:5247918..5247954,-p5@HBB
Hg19::chr12:10875643..10875687,+p@chr12:10875643..10875687
+
Hg19::chr12:25204833..25204837,+p26@LRMP
Hg19::chr15:77973117..77973119,+p@chr15:77973117..77973119
+
Hg19::chr16:223575..223610,+p@chr16:223575..223610
+
Hg19::chr16:223611..223622,+p@chr16:223611..223622
+
Hg19::chr17:47302378..47302387,-p@chr17:47302378..47302387
-
Hg19::chr19:7755354..7755360,-p@chr19:7755354..7755360
-
Hg19::chr1:172425609..172425633,-p@chr1:172425609..172425633
-
Hg19::chr1:28906381..28906392,-p3@SNORA61
Hg19::chr21:35902242..35902243,+p@chr21:35902242..35902243
+
Hg19::chr5:86705141..86705152,-p@chr5:86705141..86705152
-
Hg19::chr7:141998622..141998625,+p7@TRBV1
Hg19::chr7:150233619..150233622,+p@chr7:150233619..150233622
+
Hg19::chr8:21924232..21924243,+p27@EPB49
Hg19::chr9:21031599..21031600,-p3@PTPLAD2
Hg19::chr9:77567516..77567525,-p10@C9orf40
Hg19::chrX:133894375..133894379,-p1@ENST00000363050


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:0006906vesicle fusion0.0169630723455826
GO:0007516hemocyte development0.0169630723455826
GO:0042386hemocyte differentiation0.0169630723455826
GO:0006903vesicle targeting0.0169630723455826
GO:0051650establishment of vesicle localization0.0169630723455826
GO:0051648vesicle localization0.0169630723455826
GO:0007010cytoskeleton organization and biogenesis0.0169630723455826
GO:0051017actin filament bundle formation0.0169630723455826
GO:0051693actin filament capping0.0169630723455826
GO:0051016barbed-end actin filament capping0.0169630723455826
GO:0030835negative regulation of actin filament depolymerization0.0169630723455826
GO:0030834regulation of actin filament depolymerization0.0169630723455826
GO:0030042actin filament depolymerization0.0169630723455826
GO:0051656establishment of organelle localization0.0169630723455826
GO:0005344oxygen transporter activity0.0179282200907595
GO:0005833hemoglobin complex0.0179282200907595
GO:0015671oxygen transport0.0179282200907595
GO:0015669gas transport0.0179282200907595
GO:0051640organelle localization0.0179282200907595
GO:0006944membrane fusion0.0186518664011759
GO:0007015actin filament organization0.0186518664011759
GO:0008064regulation of actin polymerization and/or depolymerization0.0186518664011759
GO:0051261protein depolymerization0.0186518664011759
GO:0030832regulation of actin filament length0.0186518664011759
GO:0032535regulation of cellular component size0.0186518664011759
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0186518664011759
GO:0051129negative regulation of cellular component organization and biogenesis0.0195985291444856
GO:0051493regulation of cytoskeleton organization and biogenesis0.0195985291444856
GO:0033043regulation of organelle organization and biogenesis0.0195985291444856
GO:0019825oxygen binding0.0195985291444856
GO:0008154actin polymerization and/or depolymerization0.0202948970506126
GO:0006996organelle organization and biogenesis0.0214567854777106
GO:0051128regulation of cellular component organization and biogenesis0.0312180513871598
GO:0051248negative regulation of protein metabolic process0.0315081544032493
GO:0005737cytoplasm0.0357002929817791
GO:0030097hemopoiesis0.0459898790239126
GO:0048534hemopoietic or lymphoid organ development0.0480650732299859
GO:0002520immune system development0.0492218306408048



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
blood1.48e-4915
haemolymphatic fluid1.48e-4915
organism substance1.48e-4915
adult organism2.02e-18114
lower lobe of right lung6.82e-131
right lung lobe6.82e-131
lower lobe of lung6.82e-131
lobe of lung6.82e-131
right lung6.82e-131
dura mater9.73e-131
future meninx9.73e-131
ectomeninx9.73e-131
future dura mater9.73e-131
hematopoietic system1.24e-1098
blood island1.24e-1098
hemolymphoid system1.54e-09108
hemopoietic organ1.68e-077
immune organ1.68e-077
meninx5.28e-072
membrane organ5.28e-072
meningeal cluster5.28e-072


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)
MA0003.10.57669
MA0004.12.30157
MA0006.10.285338
MA0007.10.168078
MA0009.10.561062
MA0014.10.442485
MA0017.10.697761
MA0019.10.290278
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.0924235
MA0029.10.484339
MA0030.10.474212
MA0031.10.41796
MA0038.10.25521
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.10.561349
MA0046.10.551181
MA0048.10.650948
MA0050.10.512765
MA0051.10.251994
MA0052.10.492957
MA0055.10.589179
MA0056.10
MA0057.10.619683
MA0058.10.763816
MA0059.10.760411
MA0060.10.136253
MA0061.10.0254296
MA0063.10
MA0066.11.31072
MA0067.10.858361
MA0068.10.0158377
MA0069.10.547689
MA0070.10.537571
MA0071.11.19989
MA0072.10.533514
MA0073.10.0180182
MA0074.12.00199
MA0076.10.129195
MA0077.10.526569
MA0078.10.33032
MA0081.10.37884
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.10.761703
MA0089.10
MA0090.10.138104
MA0091.10.537838
MA0092.10.157193
MA0093.12.07238
MA0095.10
MA0098.10
MA0100.10.734012
MA0101.10.294344
MA0103.10.573987
MA0105.10.0885831
MA0106.10.782788
MA0107.10.195292
MA0108.20.415325
MA0109.10
MA0111.10.146643
MA0113.10.812272
MA0114.10.0506063
MA0115.10.785493
MA0116.12.77299
MA0117.10.595385
MA0119.10.109564
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.913068
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.0959198
MA0140.10.224213
MA0141.13.14081
MA0142.10.39079
MA0143.10.300362
MA0144.10.388125
MA0145.10.402421
MA0146.12.08837
MA0147.11.6733
MA0148.10.198049
MA0149.10.620638
MA0062.20.102633
MA0035.20.223695
MA0039.20.00467442
MA0138.20.331323
MA0002.20.123692
MA0137.20.0959012
MA0104.20.912884
MA0047.20.277681
MA0112.21.07495
MA0065.20.623555
MA0150.10.134443
MA0151.10
MA0152.10.229055
MA0153.10.65174
MA0154.10.186884
MA0155.10.204379
MA0156.10.0971366
MA0157.10.367703
MA0158.10
MA0159.10.204897
MA0160.10.20889
MA0161.10
MA0162.10.0810813
MA0163.10.144812
MA0164.11.51026
MA0080.20.0856322
MA0018.20.288301
MA0099.20.229319
MA0079.20.0438786
MA0102.21.07547
MA0258.10.366495
MA0259.11.72611
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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