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Coexpression cluster:C988: Difference between revisions

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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:35, 17 September 2013


Full id: C988_pineal_small_colon_eye_renal_cerebellum_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr11:115067312..115067316,-p@chr11:115067312..115067316
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Hg19::chr11:115078302..115078307,-p@chr11:115078302..115078307
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Hg19::chr11:115211232..115211238,-p@chr11:115211232..115211238
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Hg19::chr11:115239731..115239744,-p@chr11:115239731..115239744
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Hg19::chr11:115256343..115256351,-p@chr11:115256343..115256351
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Hg19::chr11:115261379..115261392,-p@chr11:115261379..115261392
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Hg19::chr11:115278588..115278591,-p@chr11:115278588..115278591
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Hg19::chr11:115375126..115375140,-p1@CADM1


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
neural tube1.28e-4156
neural rod1.28e-4156
future spinal cord1.28e-4156
neural keel1.28e-4156
central nervous system9.58e-4081
nervous system1.62e-3989
regional part of nervous system4.11e-3953
regional part of brain4.11e-3953
brain5.34e-3668
future brain5.34e-3668
adult organism6.15e-34114
regional part of forebrain6.23e-3441
forebrain6.23e-3441
anterior neural tube6.23e-3441
future forebrain6.23e-3441
neural plate3.79e-3382
presumptive neural plate3.79e-3382
neurectoderm6.91e-3386
organ system subdivision9.69e-30223
brain grey matter3.33e-2834
gray matter3.33e-2834
ecto-epithelium8.49e-28104
telencephalon1.03e-2734
ectoderm-derived structure7.39e-27171
ectoderm7.39e-27171
presumptive ectoderm7.39e-27171
regional part of telencephalon1.84e-2632
cerebral hemisphere4.01e-2632
pre-chordal neural plate6.08e-2661
cerebral cortex6.20e-2125
pallium6.20e-2125
structure with developmental contribution from neural crest3.43e-19132
regional part of cerebral cortex9.75e-1922
neocortex5.99e-1720
anatomical cluster2.54e-15373
organ part4.60e-11218
multi-tissue structure8.69e-11342
tube1.46e-10192
organ3.72e-10503
posterior neural tube6.09e-0915
chordal neural plate6.09e-0915
anatomical conduit6.52e-09240
neural nucleus1.10e-089
nucleus of brain1.10e-089
basal ganglion1.16e-089
nuclear complex of neuraxis1.16e-089
aggregate regional part of brain1.16e-089
collection of basal ganglia1.16e-089
cerebral subcortex1.16e-089
epithelium1.00e-07306
diencephalon1.34e-077
future diencephalon1.34e-077
segmental subdivision of nervous system2.05e-0713
cell layer2.24e-07309
telencephalic nucleus5.43e-077
temporal lobe6.40e-076


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)
MA0003.10.00718652
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.0484929
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.11.12605
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.11.12793
MA0051.11.36251
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.556724
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.466265
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.12.13567
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.220937
MA0146.10.00761723
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.164269
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.141536
MA0164.11.51849
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.0171409
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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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