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{{Coexpression_clusters
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|full_id=C2606_amygdala_hippocampus_pineal_medulloblastoma_insula_frontal_nucleus
|id=C2606
}}

Latest revision as of 12:09, 17 September 2013


Full id: C2606_amygdala_hippocampus_pineal_medulloblastoma_insula_frontal_nucleus



Phase1 CAGE Peaks

Hg19::chr1:99729813..99729860,+p3@LPPR4
Hg19::chr1:99730028..99730060,+p2@LPPR4
Hg19::chr1:99730062..99730107,+p1@LPPR4
Hg19::chr1:99730122..99730131,+p4@LPPR4


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
nervous system3.34e-5089
central nervous system3.60e-5081
neural tube5.18e-4556
neural rod5.18e-4556
future spinal cord5.18e-4556
neural keel5.18e-4556
regional part of nervous system1.19e-4253
regional part of brain1.19e-4253
adult organism4.67e-42114
brain1.89e-4168
future brain1.89e-4168
regional part of forebrain3.44e-3841
forebrain3.44e-3841
anterior neural tube3.44e-3841
future forebrain3.44e-3841
neural plate1.87e-3382
presumptive neural plate1.87e-3382
telencephalon1.38e-3134
brain grey matter2.07e-3134
gray matter2.07e-3134
neurectoderm1.02e-3086
cerebral hemisphere2.73e-3032
regional part of telencephalon8.44e-3032
organ system subdivision1.19e-27223
ectoderm-derived structure4.11e-26171
ectoderm4.11e-26171
presumptive ectoderm4.11e-26171
pre-chordal neural plate1.22e-2561
cerebral cortex1.69e-2325
pallium1.69e-2325
ecto-epithelium7.14e-23104
structure with developmental contribution from neural crest2.69e-22132
regional part of cerebral cortex3.17e-2122
neocortex3.36e-1920
anatomical cluster4.36e-11373
basal ganglion7.92e-109
nuclear complex of neuraxis7.92e-109
aggregate regional part of brain7.92e-109
collection of basal ganglia7.92e-109
cerebral subcortex7.92e-109
neural nucleus2.68e-099
nucleus of brain2.68e-099
multi-tissue structure1.81e-08342
posterior neural tube2.06e-0815
chordal neural plate2.06e-0815
multi-cellular organism5.70e-08656
diencephalon6.20e-087
future diencephalon6.20e-087
telencephalic nucleus9.44e-087
organ2.12e-07503
gyrus3.14e-076
tube3.35e-07192
segmental subdivision of nervous system7.31e-0713
anatomical system7.49e-07624
anatomical group9.19e-07625
limbic system9.55e-075


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)
MA0003.11.8989
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
MA0019.12.02743
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.11.54523
MA0091.10.715356
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.11.13665
MA0115.13.20374
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.65877
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.13.02177
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.20.657636
MA0102.21.75932
MA0258.11.07498
MA0259.10.471671
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#1066445.360256373075030.001211145381643620.00817863781931193
REST#597837.237521537096020.004104697304192610.019583850239953
ZNF263#1012748.221841637010680.0002187871180958320.00249181110434139



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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