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{{Coexpression_clusters
{
|full_id=C1095_heart_skin_lung_neuroblastoma_skeletal_adipose_rectum
 

Latest revision as of 11:37, 17 September 2013


Full id: C1095_heart_skin_lung_neuroblastoma_skeletal_adipose_rectum



Phase1 CAGE Peaks

Hg19::chr8:13154787..13154792,-p@chr8:13154787..13154792
-
Hg19::chr8:13372153..13372182,-p12@DLC1
Hg19::chr8:13372233..13372251,-p15@DLC1
Hg19::chr8:13372253..13372282,-p7@DLC1
Hg19::chr8:13372298..13372312,-p24@DLC1
Hg19::chr8:13372331..13372375,-p4@DLC1
Hg19::chr8:13372410..13372429,-p9@DLC1
Hg19::chr8:13372434..13372466,-p8@DLC1


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

No GOStat results

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>

Cell Type
Ontology termp-valuen
fibroblast5.21e-1276
skin fibroblast6.94e-0823
Uber Anatomy
Ontology termp-valuen
adult organism3.80e-39114
structure with developmental contribution from neural crest4.10e-20132
neural tube6.73e-2056
neural rod6.73e-2056
future spinal cord6.73e-2056
neural keel6.73e-2056
regional part of nervous system2.88e-1853
regional part of brain2.88e-1853
regional part of forebrain1.07e-1741
forebrain1.07e-1741
anterior neural tube1.07e-1741
future forebrain1.07e-1741
neurectoderm4.29e-1786
nervous system2.88e-1689
neural plate4.31e-1682
presumptive neural plate4.31e-1682
brain5.84e-1668
future brain5.84e-1668
brain grey matter7.34e-1634
gray matter7.34e-1634
telencephalon7.34e-1634
regional part of telencephalon7.62e-1532
cerebral hemisphere9.07e-1532
central nervous system2.16e-1481
multi-tissue structure1.50e-13342
neocortex2.45e-1320
regional part of cerebral cortex5.59e-1322
tissue3.85e-12773
ectoderm-derived structure8.73e-12171
ectoderm8.73e-12171
presumptive ectoderm8.73e-12171
cerebral cortex1.35e-1125
pallium1.35e-1125
organ system subdivision3.37e-11223
pre-chordal neural plate7.51e-1161
anatomical cluster9.70e-11373
multi-cellular organism5.17e-10656
ecto-epithelium2.42e-09104
anatomical conduit1.39e-08240
cell layer3.61e-08309
epithelium9.66e-08306
tube1.47e-07192
anatomical system2.00e-07624
anatomical group2.57e-07625
primary circulatory organ7.32e-0727


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)
MA0003.10.00101002
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
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
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.835832
MA0056.10
MA0057.11.05663
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.13.68539
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.11.49247
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.11.38624
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.16.21362
MA0145.10.0613434
MA0146.10.418694
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.00133745
MA0138.20.653421
MA0002.20.179788
MA0137.23.25541
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.0535085
MA0156.13.26917
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.625961
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.200187
MA0102.21.46209
MA0258.10.209744
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
CTCF#1066474.690224326440655.26249365325459e-050.000894255734871879
EP300#203375.92719901044531.06380393527283e-050.00027623724315256
RAD21#588579.060654658524295.73112922357867e-072.64028850896045e-05
YY1#752874.297274406122129.53674534900876e-050.00136476863182396



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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