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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:52, 17 September 2013


Full id: C1782_medulloblastoma_putamen_caudate_brain_nucleus_occipital_medial



Phase1 CAGE Peaks

Hg19::chr17:45056606..45056625,-p1@RPRML
Hg19::chr17:45056637..45056648,-p2@RPRML
Hg19::chr3:164913859..164913883,-p5@SLITRK3
Hg19::chr3:164913920..164913931,-p11@SLITRK3
Hg19::chr4:186877864..186877875,-p45@SORBS2


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


No GOStat results

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
regional part of nervous system1.33e-8153
regional part of brain1.33e-8153
telencephalon1.25e-7734
cerebral hemisphere1.77e-7732
brain grey matter4.87e-7734
gray matter4.87e-7734
neural tube9.21e-7756
neural rod9.21e-7756
future spinal cord9.21e-7756
neural keel9.21e-7756
brain9.60e-7668
future brain9.60e-7668
regional part of forebrain2.06e-7241
forebrain2.06e-7241
anterior neural tube2.06e-7241
future forebrain2.06e-7241
central nervous system4.70e-7281
regional part of telencephalon7.67e-7232
nervous system5.37e-7089
regional part of cerebral cortex2.94e-6422
neocortex2.28e-5820
cerebral cortex4.00e-5625
pallium4.00e-5625
neurectoderm8.63e-5586
neural plate3.19e-5282
presumptive neural plate3.19e-5282
pre-chordal neural plate3.22e-4961
adult organism4.81e-48114
ecto-epithelium4.33e-39104
ectoderm-derived structure2.54e-36171
ectoderm2.54e-36171
presumptive ectoderm2.54e-36171
structure with developmental contribution from neural crest5.65e-34132
organ system subdivision6.32e-32223
basal ganglion1.66e-229
nuclear complex of neuraxis1.66e-229
aggregate regional part of brain1.66e-229
collection of basal ganglia1.66e-229
cerebral subcortex1.66e-229
neural nucleus8.44e-229
nucleus of brain8.44e-229
gyrus1.81e-196
tube1.07e-17192
telencephalic nucleus8.06e-177
anatomical cluster1.09e-16373
parietal lobe1.26e-165
temporal lobe1.39e-166
occipital lobe1.74e-165
limbic system1.79e-165
corpus striatum2.61e-144
striatum2.61e-144
ventral part of telencephalon2.61e-144
future corpus striatum2.61e-144
anatomical conduit5.18e-13240
brainstem5.75e-126
organ part1.31e-11218
multi-tissue structure2.60e-11342
segmental subdivision of hindbrain3.75e-1112
hindbrain3.75e-1112
presumptive hindbrain3.75e-1112
caudate-putamen4.59e-113
dorsal striatum4.59e-113
frontal cortex1.31e-103
segmental subdivision of nervous system3.20e-1013
small intestine5.89e-104
pons2.44e-093
posterior neural tube9.88e-0915
chordal neural plate9.88e-0915
epithelium9.93e-09306
cell layer1.50e-08309
embryonic structure2.32e-08564
regional part of metencephalon4.55e-089
metencephalon4.55e-089
future metencephalon4.55e-089
embryo6.08e-08592
germ layer6.90e-08560
germ layer / neural crest6.90e-08560
embryonic tissue6.90e-08560
presumptive structure6.90e-08560
germ layer / neural crest derived structure6.90e-08560
epiblast (generic)6.90e-08560
caudate nucleus8.68e-082
future caudate nucleus8.68e-082
developing anatomical structure1.02e-07581
middle temporal gyrus1.37e-072
amygdala1.84e-072
Ammon's horn1.90e-072
lobe parts of cerebral cortex1.90e-072
hippocampal formation1.90e-072
limbic lobe1.90e-072
middle frontal gyrus2.23e-072
globus pallidus3.70e-072
pallidum3.70e-072
organ3.80e-07503
meninx4.89e-072
membrane organ4.89e-072
meningeal cluster4.89e-072


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)
MA0003.11.04569
MA0004.10.626788
MA0006.10.452993
MA0007.11.47524
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
MA0042.11.48719
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.11.05691
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
MA0073.13.88786
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.11.77562
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
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
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.6031
MA0147.10.386018
MA0148.10.653474
MA0149.11.63245
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.11.66846
MA0153.11.21379
MA0154.10.514087
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.340387
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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.