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{{Coexpression_clusters
{
|full_id=C1040_smooth_aorta_heart_bladder_uterus_penis_cervix
 

Latest revision as of 11:36, 17 September 2013


Full id: C1040_smooth_aorta_heart_bladder_uterus_penis_cervix



Phase1 CAGE Peaks

Hg19::chr14:94443066..94443092,-p2@ASB2
Hg19::chr2:218843537..218843559,-p4@TNS1
Hg19::chr2:218843565..218843592,-p8@TNS1
Hg19::chr2:218843623..218843635,-p11@TNS1
Hg19::chr4:119809984..119810024,+p2@SYNPO2
Hg19::chr4:119810034..119810045,+p8@SYNPO2
Hg19::chr9:70971821..70971841,+p2@PGM5
Hg19::chrX:11683221..11683257,-p3@ARHGAP6


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:0004614phosphoglucomutase activity0.0234374204859477
GO:0004252serine-type endopeptidase activity0.0234374204859477
GO:0008236serine-type peptidase activity0.0234374204859477
GO:0017171serine hydrolase activity0.0234374204859477
GO:0030054cell junction0.0234374204859477
GO:0003779actin binding0.0234374204859477
GO:0005913cell-cell adherens junction0.0237632929688061
GO:0008092cytoskeletal protein binding0.0254837298998518
GO:0044267cellular protein metabolic process0.0254837298998518
GO:0044260cellular macromolecule metabolic process0.0254837298998518
GO:0005100Rho GTPase activator activity0.0254837298998518
GO:0005884actin filament0.0254837298998518
GO:0019538protein metabolic process0.0254837298998518
GO:0016868intramolecular transferase activity, phosphotransferases0.0264162701651135
GO:0030041actin filament polymerization0.0264162701651135
GO:0004289subtilase activity0.0272350536668043
GO:0004175endopeptidase activity0.0272350536668043
GO:0005070SH3/SH2 adaptor activity0.0347587692753149
GO:0005912adherens junction0.0362788179553529
GO:0060090molecular adaptor activity0.0370633375511242
GO:0008154actin polymerization and/or depolymerization0.0370633375511242
GO:0016866intramolecular transferase activity0.0394222340296126
GO:0008233peptidase activity0.0465675100398205
GO:0030674protein binding, bridging0.0475019981986934
GO:0006508proteolysis0.0475019981986934
GO:0051258protein polymerization0.0475019981986934



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>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.34e-55114
neural tube6.78e-1956
neural rod6.78e-1956
future spinal cord6.78e-1956
neural keel6.78e-1956
neural plate6.21e-1782
presumptive neural plate6.21e-1782
regional part of nervous system6.66e-1753
regional part of brain6.66e-1753
anatomical cluster1.41e-16373
neurectoderm2.12e-1586
central nervous system7.32e-1581
multi-tissue structure1.42e-14342
structure with developmental contribution from neural crest1.70e-14132
brain2.75e-1468
future brain2.75e-1468
organ system subdivision1.47e-13223
telencephalon5.61e-1334
regional part of forebrain1.29e-1241
forebrain1.29e-1241
anterior neural tube1.29e-1241
future forebrain1.29e-1241
brain grey matter1.55e-1234
gray matter1.55e-1234
nervous system1.58e-1289
cerebral hemisphere7.70e-1232
regional part of telencephalon1.25e-1132
anatomical conduit3.36e-11240
ecto-epithelium6.97e-11104
pre-chordal neural plate2.75e-1061
cerebral cortex4.78e-1025
pallium4.78e-1025
multi-cellular organism1.94e-09656
organ2.07e-09503
tube4.96e-09192
epithelium7.43e-09306
regional part of cerebral cortex1.07e-0822
neocortex1.26e-0820
cell layer1.61e-08309
posterior neural tube9.46e-0815
chordal neural plate9.46e-0815
anatomical system1.36e-07624
ectoderm-derived structure1.56e-07171
ectoderm1.56e-07171
presumptive ectoderm1.56e-07171
anatomical group1.66e-07625
embryo1.94e-07592
organ part3.54e-07218
developing anatomical structure5.88e-07581


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)
MA0003.11.34332
MA0004.11.15451
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.275152
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.12.12623
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.12.19078
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.466265
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.12.13567
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.11.07975
MA0093.12.26508
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.291333
MA0105.17.30325
MA0106.10.59853
MA0107.11.23931
MA0108.20.753643
MA0109.10
MA0111.11.04489
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.11.63558
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.12.21469
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.10.220937
MA0146.10.418694
MA0147.10.243042
MA0148.10.480298
MA0149.127.1036
MA0062.20.161302
MA0035.21.28264
MA0039.20.0325944
MA0138.20.653421
MA0002.20.179788
MA0137.20.86081
MA0104.20.55506
MA0047.20.586412
MA0112.20.0572179
MA0065.21.78056
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.14.06872
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.12.76433
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.609448
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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
CTBP2#1488323.5188751272480.0002135706294477470.00246166018859875



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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