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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:49, 17 September 2013


Full id: C1654_smallcell_cord_small_B_Neural_gastrointestinal_splenic



Phase1 CAGE Peaks

Hg19::chr12:103351813..103351844,+p4@ASCL1
Hg19::chr12:103352277..103352324,+p2@ASCL1
Hg19::chr12:103352326..103352351,+p3@ASCL1
Hg19::chr12:103352595..103352622,+p@chr12:103352595..103352622
+
Hg19::chr3:179754677..179754701,-p5@PEX5L


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:0060163subpallium neuron fate commitment0.000804584167353507
GO:0014017neuroblast fate commitment0.000804584167353507
GO:0014016neuroblast differentiation0.000804584167353507
GO:0007400neuroblast fate determination0.000804584167353507
GO:0060165regulation of timing of subpallium neuron differentiation0.000804584167353507
GO:0060164regulation of timing of neuron differentiation0.000804584167353507
GO:0021544subpallium development0.00206886981320192
GO:0048505regulation of timing of cell differentiation0.00214546304184275
GO:0040034regulation of development, heterochronic0.00214546304184275
GO:0021537telencephalon development0.00530947391795865
GO:0048663neuron fate commitment0.00614292166841388
GO:0007405neuroblast proliferation0.0068373548804725
GO:0045664regulation of neuron differentiation0.00932932998797643
GO:0010001glial cell differentiation0.00932932998797643
GO:0001709cell fate determination0.00932932998797643
GO:0042063gliogenesis0.0102176854681714
GO:0001764neuron migration0.0102176854681714
GO:0030900forebrain development0.0123287861003839
GO:0007219Notch signaling pathway0.0126947983978901
GO:0045165cell fate commitment0.0171199860133783
GO:0007389pattern specification process0.0284536626285139
GO:0007420brain development0.0301607648054761
GO:0045595regulation of cell differentiation0.0301607648054761
GO:0048666neuron development0.0309067338413351
GO:0030182neuron differentiation0.0401418013441119
GO:0016477cell migration0.0401418013441119
GO:0007417central nervous system development0.0401418013441119
GO:0050793regulation of developmental process0.0401418013441119
GO:0048699generation of neurons0.0401418013441119
GO:0022008neurogenesis0.0419982514204205



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 tube1.13e-8656
neural rod1.13e-8656
future spinal cord1.13e-8656
neural keel1.13e-8656
nervous system1.88e-8089
regional part of nervous system3.02e-8053
regional part of brain3.02e-8053
central nervous system8.76e-7881
regional part of forebrain5.79e-7141
forebrain5.79e-7141
anterior neural tube5.79e-7141
future forebrain5.79e-7141
brain grey matter3.99e-6534
gray matter3.99e-6534
brain4.06e-6568
future brain4.06e-6568
telencephalon5.92e-6534
cerebral hemisphere3.43e-6132
regional part of telencephalon7.38e-6132
neural plate3.10e-6082
presumptive neural plate3.10e-6082
neurectoderm8.48e-5786
pre-chordal neural plate1.08e-4961
cerebral cortex7.85e-4825
pallium7.85e-4825
regional part of cerebral cortex1.06e-4622
ecto-epithelium1.53e-46104
neocortex3.22e-4220
ectoderm-derived structure1.21e-37171
ectoderm1.21e-37171
presumptive ectoderm1.21e-37171
adult organism3.23e-36114
structure with developmental contribution from neural crest2.16e-35132
organ system subdivision3.78e-35223
tube4.05e-20192
neural nucleus2.54e-189
nucleus of brain2.54e-189
basal ganglion2.66e-189
nuclear complex of neuraxis2.66e-189
aggregate regional part of brain2.66e-189
collection of basal ganglia2.66e-189
cerebral subcortex2.66e-189
posterior neural tube1.34e-1615
chordal neural plate1.34e-1615
anatomical cluster1.47e-15373
gyrus1.96e-146
telencephalic nucleus3.11e-147
brainstem5.22e-146
organ part2.02e-13218
anatomical conduit2.15e-13240
segmental subdivision of nervous system6.43e-1313
occipital lobe1.62e-125
parietal lobe2.16e-125
temporal lobe3.57e-126
limbic system3.80e-125
segmental subdivision of hindbrain3.65e-1112
hindbrain3.65e-1112
presumptive hindbrain3.65e-1112
epithelium1.29e-10306
cell layer2.22e-10309
corpus striatum6.08e-094
striatum6.08e-094
ventral part of telencephalon6.08e-094
future corpus striatum6.08e-094
multi-tissue structure1.41e-08342
frontal cortex2.90e-083
medulla oblongata5.41e-083
myelencephalon5.41e-083
future myelencephalon5.41e-083
diencephalon5.74e-087
future diencephalon5.74e-087
spinal cord9.08e-083
dorsal region element9.08e-083
dorsum9.08e-083
pons1.09e-073
germ layer3.38e-07560
germ layer / neural crest3.38e-07560
embryonic tissue3.38e-07560
presumptive structure3.38e-07560
germ layer / neural crest derived structure3.38e-07560
epiblast (generic)3.38e-07560
embryonic structure5.09e-07564
caudate-putamen5.79e-073
dorsal striatum5.79e-073
developing anatomical structure9.57e-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)
MA0003.11.40197
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.14.04387
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.126.0505
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.868598
MA0146.10.333008
MA0147.11.00307
MA0148.10.653474
MA0149.11.63245
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0850863
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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#1066444.288205098460020.005152015588243280.0239227883701111
SUZ12#23512330.06946854663777.70283100694034e-050.00118811987525305



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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