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Coexpression cluster:C3042: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3042_optic_cerebellum_temporal_skeletal_occipital_parietal_globus
|id=C3042
}}

Latest revision as of 12:18, 17 September 2013


Full id: C3042_optic_cerebellum_temporal_skeletal_occipital_parietal_globus



Phase1 CAGE Peaks

Hg19::chr10:735553..735647,-p1@DIP2C
Hg19::chr10:735808..735834,-p2@DIP2C
Hg19::chr1:10270585..10270614,+p2@KIF1B


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:0008089anterograde axon cargo transport0.00980103585557702
GO:0008088axon cargo transport0.00980103585557702
GO:0019894kinesin binding0.00980103585557702
GO:0007274neuromuscular synaptic transmission0.00980103585557702
GO:0007270nerve-nerve synaptic transmission0.016550423946942



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
neurectodermal cell9.06e-0859
Uber Anatomy
Ontology termp-valuen
nervous system9.87e-3889
central nervous system5.97e-3681
neural tube5.91e-3456
neural rod5.91e-3456
future spinal cord5.91e-3456
neural keel5.91e-3456
ectoderm-derived structure1.45e-32171
ectoderm1.45e-32171
presumptive ectoderm1.45e-32171
adult organism2.07e-32114
regional part of nervous system5.02e-3253
regional part of brain5.02e-3253
brain1.43e-3168
future brain1.43e-3168
neurectoderm2.30e-3186
neural plate7.96e-3182
presumptive neural plate7.96e-3182
structure with developmental contribution from neural crest5.45e-26132
regional part of forebrain1.42e-2541
forebrain1.42e-2541
anterior neural tube1.42e-2541
future forebrain1.42e-2541
ecto-epithelium7.57e-25104
brain grey matter6.91e-2234
gray matter6.91e-2234
pre-chordal neural plate6.93e-2261
telencephalon7.77e-2234
regional part of telencephalon1.37e-2032
cerebral hemisphere1.71e-2032
organ system subdivision2.06e-20223
anatomical cluster8.76e-20373
multi-cellular organism1.16e-19656
multi-tissue structure1.03e-16342
cerebral cortex4.51e-1625
pallium4.51e-1625
regional part of cerebral cortex3.57e-1522
anatomical conduit1.10e-14240
anatomical system1.82e-14624
cell layer1.97e-14309
anatomical group3.11e-14625
epithelium3.40e-14306
neocortex5.64e-1420
tube9.31e-14192
embryo2.35e-12592
organ1.36e-11503
developing anatomical structure5.19e-11581
organ part2.33e-10218
germ layer4.77e-10560
germ layer / neural crest4.77e-10560
embryonic tissue4.77e-10560
presumptive structure4.77e-10560
germ layer / neural crest derived structure4.77e-10560
epiblast (generic)4.77e-10560
embryonic structure9.14e-10564
posterior neural tube1.99e-0915
chordal neural plate1.99e-0915
segmental subdivision of nervous system2.56e-0813
segmental subdivision of hindbrain1.22e-0712
hindbrain1.22e-0712
presumptive hindbrain1.22e-0712
neural nucleus2.76e-079
nucleus of brain2.76e-079
basal ganglion3.62e-079
nuclear complex of neuraxis3.62e-079
aggregate regional part of brain3.62e-079
collection of basal ganglia3.62e-079
cerebral subcortex3.62e-079


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)
MA0003.17.68548
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.16.45108
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
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.36698
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0145.11.37817
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.14.77883
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.61229
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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