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

Latest revision as of 12:20, 17 September 2013


Full id: C3151_neuroblastoma_pineal_rectum_duodenum_caudate_locus_submaxillary



Phase1 CAGE Peaks

Hg19::chr11:43290911..43290922,-p2@HNRNPKP3
Hg19::chr11:43290929..43290949,-p1@HNRNPKP3
Hg19::chr2:113251697..113251704,+p16@TTL


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:0030516regulation of axon extension0.0137613328623572
GO:0048675axon extension0.0137613328623572
GO:0050770regulation of axonogenesis0.013923230896032
GO:0050767regulation of neurogenesis0.013923230896032
GO:0004835tubulin-tyrosine ligase activity0.013923230896032
GO:0000226microtubule cytoskeleton organization and biogenesis0.0191579339848503
GO:0007409axonogenesis0.0191579339848503
GO:0048667neuron morphogenesis during differentiation0.0191579339848503
GO:0048812neurite morphogenesis0.0191579339848503
GO:0000904cellular morphogenesis during differentiation0.0191579339848503
GO:0031175neurite development0.0191579339848503
GO:0030955potassium ion binding0.0191579339848503
GO:0048666neuron development0.0191786901430137
GO:0032990cell part morphogenesis0.0195896620746497
GO:0030030cell projection organization and biogenesis0.0195896620746497
GO:0048858cell projection morphogenesis0.0195896620746497
GO:0030182neuron differentiation0.0195896620746497
GO:0031420alkali metal ion binding0.0195896620746497
GO:0050793regulation of developmental process0.0195896620746497
GO:0048699generation of neurons0.0195896620746497
GO:0022008neurogenesis0.0201987070584739
GO:0016881acid-amino acid ligase activity0.0220034145767102
GO:0007017microtubule-based process0.022172991568504
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0250267377055614
GO:0000287magnesium ion binding0.0286619481839074
GO:0032989cellular structure morphogenesis0.0286619481839074
GO:0000902cell morphogenesis0.0286619481839074
GO:0016874ligase activity0.0374100099241392
GO:0007010cytoskeleton organization and biogenesis0.0382972590003126
GO:0007399nervous system development0.0386396640370501



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neural tube1.42e-6256
neural rod1.42e-6256
future spinal cord1.42e-6256
neural keel1.42e-6256
regional part of nervous system6.30e-6253
regional part of brain6.30e-6253
nervous system1.20e-5689
central nervous system8.41e-5381
regional part of forebrain2.69e-5141
forebrain2.69e-5141
anterior neural tube2.69e-5141
future forebrain2.69e-5141
brain2.22e-4968
future brain2.22e-4968
neurectoderm7.43e-4486
neural plate2.02e-4382
presumptive neural plate2.02e-4382
telencephalon5.52e-3834
brain grey matter5.77e-3834
gray matter5.77e-3834
adult organism3.19e-36114
pre-chordal neural plate1.12e-3561
ecto-epithelium1.04e-32104
cerebral hemisphere2.71e-3232
regional part of telencephalon3.83e-3232
ectoderm-derived structure4.46e-31171
ectoderm4.46e-31171
presumptive ectoderm4.46e-31171
organ system subdivision4.44e-26223
structure with developmental contribution from neural crest6.01e-26132
regional part of cerebral cortex2.03e-2322
neocortex1.21e-2120
neural nucleus1.56e-219
nucleus of brain1.56e-219
cerebral cortex2.07e-2025
pallium2.07e-2025
regional part of diencephalon1.30e-174
gyrus8.56e-176
tube1.06e-16192
brainstem1.46e-166
basal ganglion4.59e-169
nuclear complex of neuraxis4.59e-169
aggregate regional part of brain4.59e-169
collection of basal ganglia4.59e-169
cerebral subcortex4.59e-169
anatomical cluster1.26e-15373
diencephalon2.59e-157
future diencephalon2.59e-157
telencephalic nucleus1.39e-147
anatomical conduit7.40e-13240
pons1.59e-123
posterior neural tube2.10e-1215
chordal neural plate2.10e-1215
segmental subdivision of hindbrain1.29e-1112
hindbrain1.29e-1112
presumptive hindbrain1.29e-1112
segmental subdivision of nervous system1.13e-1013
multi-tissue structure3.27e-10342
corpus striatum4.21e-104
striatum4.21e-104
ventral part of telencephalon4.21e-104
future corpus striatum4.21e-104
pineal body5.07e-102
regional part of epithalamus5.07e-102
secretory circumventricular organ5.07e-102
circumventricular organ5.07e-102
epithalamus5.07e-102
caudate nucleus1.30e-092
future caudate nucleus1.30e-092
temporal lobe1.44e-096
dorsal plus ventral thalamus2.53e-092
thalamic complex2.53e-092
middle temporal gyrus3.12e-092
locus ceruleus3.53e-092
brainstem nucleus3.53e-092
hindbrain nucleus3.53e-092
organ part9.62e-09218
sympathetic nervous system1.59e-085
autonomic nervous system1.59e-085
epithelium2.48e-08306
cell layer3.54e-08309
limbic system4.35e-085
regional part of metencephalon2.36e-079
metencephalon2.36e-079
future metencephalon2.36e-079
developing anatomical structure3.95e-07581
germ layer4.18e-07560
germ layer / neural crest4.18e-07560
embryonic tissue4.18e-07560
presumptive structure4.18e-07560
germ layer / neural crest derived structure4.18e-07560
epiblast (generic)4.18e-07560
embryonic structure5.52e-07564
embryo8.26e-07592
Disease
Ontology termp-valuen
neuroendocrine tumor3.66e-076
neuroectodermal tumor5.99e-0710


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0042.11.89908
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
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
MA0073.10.0185922
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
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
MA0105.10.31555
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.12.04956
MA0062.21.141
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.22.08438
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
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.