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{{Coexpression_clusters
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|full_id=C1414_Wilms_cerebellum_parietal_hippocampus_medial_caudate_middle
|id=C1414
}}

Latest revision as of 11:44, 17 September 2013


Full id: C1414_Wilms_cerebellum_parietal_hippocampus_medial_caudate_middle



Phase1 CAGE Peaks

Hg19::chr15:88740321..88740326,-p@chr15:88740321..88740326
-
Hg19::chr15:88799384..88799430,-p3@NTRK3
Hg19::chr15:88799702..88799755,-p5@NTRK3
Hg19::chr15:88799926..88799941,-p2@NTRK3
Hg19::chr15:88799948..88799977,-p1@NTRK3
Hg19::chr7:54609955..54609962,+p13@VSTM2A


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:0043121neurotrophin binding0.00853644177557988



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 organism3.85e-57114
central nervous system1.08e-5581
nervous system1.12e-5489
neural tube2.52e-5256
neural rod2.52e-5256
future spinal cord2.52e-5256
neural keel2.52e-5256
regional part of nervous system1.43e-4953
regional part of brain1.43e-4953
brain3.36e-4768
future brain3.36e-4768
neural plate1.19e-4282
presumptive neural plate1.19e-4282
neurectoderm1.41e-4086
regional part of forebrain1.97e-3941
forebrain1.97e-3941
anterior neural tube1.97e-3941
future forebrain1.97e-3941
structure with developmental contribution from neural crest1.59e-35132
brain grey matter2.27e-3434
gray matter2.27e-3434
telencephalon2.70e-3434
ectoderm-derived structure7.23e-33171
ectoderm7.23e-33171
presumptive ectoderm7.23e-33171
cerebral hemisphere1.10e-3232
regional part of telencephalon1.61e-3232
ecto-epithelium5.36e-32104
pre-chordal neural plate4.46e-2961
cerebral cortex4.95e-2625
pallium4.95e-2625
organ system subdivision8.71e-26223
regional part of cerebral cortex6.33e-2422
neocortex7.13e-2220
anatomical cluster3.51e-20373
tube7.00e-16192
posterior neural tube1.35e-1315
chordal neural plate1.35e-1315
anatomical conduit9.20e-13240
segmental subdivision of nervous system7.68e-1213
multi-tissue structure1.05e-11342
segmental subdivision of hindbrain4.55e-1112
hindbrain4.55e-1112
presumptive hindbrain4.55e-1112
organ3.25e-10503
organ part4.28e-10218
basal ganglion5.62e-109
nuclear complex of neuraxis5.62e-109
aggregate regional part of brain5.62e-109
collection of basal ganglia5.62e-109
cerebral subcortex5.62e-109
neural nucleus1.06e-099
nucleus of brain1.06e-099
embryo1.33e-09592
multi-cellular organism7.63e-09656
regional part of metencephalon1.86e-089
metencephalon1.86e-089
future metencephalon1.86e-089
temporal lobe2.47e-086
cell layer3.10e-08309
developing anatomical structure4.48e-08581
telencephalic nucleus6.39e-087
embryonic structure7.97e-08564
germ layer8.03e-08560
germ layer / neural crest8.03e-08560
embryonic tissue8.03e-08560
presumptive structure8.03e-08560
germ layer / neural crest derived structure8.03e-08560
epiblast (generic)8.03e-08560
epithelium9.92e-08306
gyrus1.81e-076
brainstem6.72e-076
anatomical system8.33e-07624


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)
MA0003.11.37104
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.22849
MA0056.10
MA0057.13.49991
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.72313
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.118.4982
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.12.21033
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.115.4296
MA0062.20.23336
MA0035.20.621793
MA0039.21.86512
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.332548
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.11.09123
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.215.4802
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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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