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{{Coexpression_clusters
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|full_id=C3186_putamen_cerebellum_acute_caudate_brain_amygdala_temporal
|gostat_on_coexpression_clusters=GO:0006510!ATP-dependent proteolysis!0.0153822753973291!164832$GO:0005246!calcium channel regulator activity!0.0153822753973291!9379$GO:0004176!ATP-dependent peptidase activity!0.0153822753973291!164832$GO:0007416!synaptogenesis!0.0188282299490645!9379$GO:0016247!channel regulator activity!0.0188282299490645!9379$GO:0050808!synapse organization and biogenesis!0.0188282299490645!9379$GO:0007269!neurotransmitter secretion!0.0188282299490645!9379$GO:0045055!regulated secretory pathway!0.0218247999485838!9379$GO:0003001!generation of a signal involved in cell-cell signaling!0.0251450577024572!9379$GO:0001505!regulation of neurotransmitter levels!0.0251450577024572!9379$GO:0043062!extracellular structure organization and biogenesis!0.0251450577024572!9379
|id=C3186
}}

Latest revision as of 12:21, 17 September 2013


Full id: C3186_putamen_cerebellum_acute_caudate_brain_amygdala_temporal



Phase1 CAGE Peaks

Hg19::chr11:64411156..64411192,-p5@NRXN2
Hg19::chr11:64411195..64411222,-p6@NRXN2
Hg19::chr2:100938957..100938968,-p4@LONRF2


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:0006510ATP-dependent proteolysis0.0153822753973291
GO:0005246calcium channel regulator activity0.0153822753973291
GO:0004176ATP-dependent peptidase activity0.0153822753973291
GO:0007416synaptogenesis0.0188282299490645
GO:0016247channel regulator activity0.0188282299490645
GO:0050808synapse organization and biogenesis0.0188282299490645
GO:0007269neurotransmitter secretion0.0188282299490645
GO:0045055regulated secretory pathway0.0218247999485838
GO:0003001generation of a signal involved in cell-cell signaling0.0251450577024572
GO:0001505regulation of neurotransmitter levels0.0251450577024572
GO:0043062extracellular structure organization and biogenesis0.0251450577024572



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
neural tube2.56e-5756
neural rod2.56e-5756
future spinal cord2.56e-5756
neural keel2.56e-5756
central nervous system4.25e-5481
regional part of nervous system1.77e-5353
regional part of brain1.77e-5353
nervous system4.04e-5289
adult organism3.45e-49114
brain1.03e-4568
future brain1.03e-4568
regional part of forebrain4.15e-4541
forebrain4.15e-4541
anterior neural tube4.15e-4541
future forebrain4.15e-4541
telencephalon1.49e-4134
brain grey matter1.76e-4134
gray matter1.76e-4134
neural plate2.26e-4082
presumptive neural plate2.26e-4082
cerebral hemisphere2.21e-3932
neurectoderm4.26e-3986
regional part of telencephalon6.02e-3932
regional part of cerebral cortex4.04e-3422
neocortex3.66e-3120
ecto-epithelium9.43e-31104
pre-chordal neural plate1.69e-2961
cerebral cortex3.44e-2925
pallium3.44e-2925
ectoderm-derived structure8.39e-26171
ectoderm8.39e-26171
presumptive ectoderm8.39e-26171
structure with developmental contribution from neural crest2.49e-25132
organ system subdivision4.31e-24223
basal ganglion3.41e-149
nuclear complex of neuraxis3.41e-149
aggregate regional part of brain3.41e-149
collection of basal ganglia3.41e-149
cerebral subcortex3.41e-149
neural nucleus1.11e-139
nucleus of brain1.11e-139
posterior neural tube5.02e-1315
chordal neural plate5.02e-1315
anatomical cluster5.25e-13373
temporal lobe1.47e-116
telencephalic nucleus2.96e-117
tube4.62e-11192
gyrus4.62e-106
segmental subdivision of hindbrain1.34e-0912
hindbrain1.34e-0912
presumptive hindbrain1.34e-0912
anatomical conduit2.20e-09240
limbic system5.41e-095
brainstem5.53e-096
organ part7.00e-09218
segmental subdivision of nervous system1.10e-0813
parietal lobe1.16e-085
occipital lobe1.33e-085
corpus striatum9.15e-084
striatum9.15e-084
ventral part of telencephalon9.15e-084
future corpus striatum9.15e-084
multi-tissue structure1.14e-07342


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)
MA0003.11.0927
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.12.37462
MA0148.10.854239
MA0149.12.04956
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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
MYC#460935.22228187160940.007020843755740150.0293299960402298



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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