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

Latest revision as of 11:30, 17 September 2013


Full id: C774_neuroblastoma_optic_medulloblastoma_rhabdomyosarcoma_corpus_thyroid_acute



Phase1 CAGE Peaks

Hg19::chr4:96410648..96410672,-p@chr4:96410648..96410672
-
Hg19::chr4:96446743..96446748,-p@chr4:96446743..96446748
-
Hg19::chr4:96454053..96454065,-p@chr4:96454053..96454065
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Hg19::chr4:96470108..96470130,-p1@UNC5C
Hg19::chr4:96470148..96470181,-p3@UNC5C
Hg19::chr4:96470224..96470247,-p5@UNC5C
Hg19::chr4:96470248..96470259,-p6@UNC5C
Hg19::chr4:96470279..96470333,+p1@BC041657
Hg19::chr4:96470350..96470373,-p2@UNC5C
Hg19::chr4:96470381..96470386,-p7@UNC5C
Hg19::chr4:96470495..96470515,+p2@BC041657


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:0005042netrin receptor activity0.00335570469798658
GO:0007411axon guidance0.0194351230425056
GO:0030334regulation of cell migration0.0194351230425056
GO:0051270regulation of cell motility0.0194351230425056
GO:0040012regulation of locomotion0.0194351230425056
GO:0040011locomotion0.0194351230425056
GO:0007409axonogenesis0.0194351230425056
GO:0048667neuron morphogenesis during differentiation0.0194351230425056
GO:0048812neurite morphogenesis0.0194351230425056
GO:0000904cellular morphogenesis during differentiation0.0194351230425056
GO:0031175neurite development0.0194351230425056
GO:0007420brain development0.0194351230425056
GO:0048666neuron development0.0198760970573051
GO:0032990cell part morphogenesis0.0203020134228188
GO:0030030cell projection organization and biogenesis0.0203020134228188
GO:0048858cell projection morphogenesis0.0203020134228188
GO:0030182neuron differentiation0.0203020134228188
GO:0016477cell migration0.0203020134228188
GO:0007417central nervous system development0.0203020134228188
GO:0048699generation of neurons0.0203020134228188
GO:0022008neurogenesis0.0209332054969639
GO:0051674localization of cell0.0279398891158447
GO:0006928cell motility0.0279398891158447
GO:0032989cellular structure morphogenesis0.0320805369127517
GO:0000902cell morphogenesis0.0320805369127517
GO:0007399nervous system development0.046205472379969



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
adult organism1.27e-59114
neural tube1.59e-5256
neural rod1.59e-5256
future spinal cord1.59e-5256
neural keel1.59e-5256
regional part of nervous system5.68e-4953
regional part of brain5.68e-4953
neural plate2.58e-4682
presumptive neural plate2.58e-4682
nervous system4.51e-4689
brain6.40e-4668
future brain6.40e-4668
central nervous system1.44e-4581
neurectoderm4.17e-4386
regional part of forebrain1.19e-3841
forebrain1.19e-3841
anterior neural tube1.19e-3841
future forebrain1.19e-3841
structure with developmental contribution from neural crest6.45e-35132
telencephalon4.40e-3434
brain grey matter7.74e-3434
gray matter7.74e-3434
ecto-epithelium4.52e-33104
pre-chordal neural plate9.02e-3361
cerebral hemisphere1.41e-3132
regional part of telencephalon1.48e-3132
organ system subdivision1.20e-29223
regional part of cerebral cortex5.27e-2822
ectoderm-derived structure5.62e-26171
ectoderm5.62e-26171
presumptive ectoderm5.62e-26171
neocortex2.01e-2520
cerebral cortex9.90e-2425
pallium9.90e-2425
anatomical cluster1.83e-22373
tube1.44e-14192
posterior neural tube1.58e-1415
chordal neural plate1.58e-1415
multi-tissue structure2.42e-14342
anatomical conduit4.21e-14240
segmental subdivision of nervous system1.67e-1213
organ part9.73e-12218
basal ganglion1.27e-119
nuclear complex of neuraxis1.27e-119
aggregate regional part of brain1.27e-119
collection of basal ganglia1.27e-119
cerebral subcortex1.27e-119
organ1.30e-11503
neural nucleus1.40e-119
nucleus of brain1.40e-119
segmental subdivision of hindbrain3.09e-1112
hindbrain3.09e-1112
presumptive hindbrain3.09e-1112
temporal lobe1.67e-096
telencephalic nucleus2.34e-097
epithelium1.15e-08306
embryo2.14e-08592
cell layer2.28e-08309
regional part of metencephalon2.46e-089
metencephalon2.46e-089
future metencephalon2.46e-089
gyrus3.21e-086
brainstem4.56e-086
developing anatomical structure5.58e-08581
embryonic structure8.02e-08564
germ layer1.03e-07560
germ layer / neural crest1.03e-07560
embryonic tissue1.03e-07560
presumptive structure1.03e-07560
germ layer / neural crest derived structure1.03e-07560
epiblast (generic)1.03e-07560
limbic system1.11e-075
occipital lobe2.61e-075
parietal lobe3.12e-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)
MA0003.10.00460185
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.114225
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.11.97347
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.12.66834
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.111.4732
MA0056.10
MA0057.10.397382
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.12.54939
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.141.9939
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.0234479
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.10.0403209
MA0106.10.482519
MA0107.10.924453
MA0108.20.630531
MA0109.10
MA0111.11.48644
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.11.57257
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.02761
MA0146.10.00165539
MA0147.10.162359
MA0148.10.372124
MA0149.14.78656
MA0062.20.0969238
MA0035.20.404774
MA0039.22.45422
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.0251803
MA0065.20.28513
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.11.09568
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.12.1547
MA0163.17.52257
MA0164.12.19328
MA0080.21.15057
MA0018.22.1073
MA0099.20.411824
MA0079.211.4408
MA0102.21.32663
MA0258.10.135061
MA0259.11.54967
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
CTBP2#1488528.50772742696734.38027279281381e-072.08986436824432e-05
CTCF#1066483.898368271327290.0001406611760594710.00183470870069628
RAD21#588587.530933742150069.5260786570561e-074.0690966415717e-05
REST#597887.018202702638561.64058660363651e-066.21928218864587e-05
YY1#752883.571760545348260.0002682005866906720.00286553463666364
ZNF263#1012785.979521190553225.60369437973428e-060.000168999202230745



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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