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Coexpression cluster:C2733: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;6.84463,MA0004.1;0.71247,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.86845,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;1.35734,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;6.69514,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;4.83833,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;2.50216,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;1.43218,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;3.57792,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.912459,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.8309,MA0147.1;5.25242,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.931615,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;7.08088,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;1.21162,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;2.15942,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;2.02192,MA0099.2;0.7872,MA0079.2;0.327251,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;3.06353,MA0442.1;0
}}
}}

Revision as of 20:52, 22 January 2013


Full id: C2733_small_medial_medulloblastoma_paracentral_frontal_parietal_smallcell



Phase1 CAGE Peaks

Hg19::chr3:179754706..179754732,-p4@PEX5L
Hg19::chr3:179754733..179754773,-p3@PEX5L
Hg19::chr3:179754789..179754804,-p6@PEX5L
Hg19::chr3:179754806..179754872,-p2@PEX5L


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
nervous system5.74e-5989
neural tube2.92e-5756
neural rod2.92e-5756
future spinal cord2.92e-5756
neural keel2.92e-5756
central nervous system2.93e-5681
regional part of nervous system2.33e-5353
regional part of brain2.33e-5353
brain1.01e-4968
future brain1.01e-4968
regional part of forebrain4.56e-4641
forebrain4.56e-4641
anterior neural tube4.56e-4641
future forebrain4.56e-4641
neural plate1.72e-4082
presumptive neural plate1.72e-4082
telencephalon2.32e-4034
brain grey matter3.08e-4034
gray matter3.08e-4034
neurectoderm2.89e-3986
cerebral hemisphere5.69e-3832
regional part of telencephalon1.46e-3732
adult organism1.89e-35114
regional part of cerebral cortex4.72e-3422
pre-chordal neural plate9.82e-3461
ecto-epithelium2.33e-33104
neocortex3.34e-3120
cerebral cortex4.12e-2925
pallium4.12e-2925
ectoderm-derived structure4.00e-28171
ectoderm4.00e-28171
presumptive ectoderm4.00e-28171
structure with developmental contribution from neural crest3.03e-25132
organ system subdivision1.55e-24223
basal ganglion9.29e-139
nuclear complex of neuraxis9.29e-139
aggregate regional part of brain9.29e-139
collection of basal ganglia9.29e-139
cerebral subcortex9.29e-139
neural nucleus1.85e-129
nucleus of brain1.85e-129
posterior neural tube3.49e-1215
chordal neural plate3.49e-1215
temporal lobe3.46e-116
tube4.75e-11192
gyrus1.39e-106
segmental subdivision of nervous system5.66e-1013
epithelium5.91e-10306
telencephalic nucleus7.26e-107
cell layer1.17e-09309
brainstem2.21e-096
anatomical cluster3.13e-09373
parietal lobe8.24e-095
limbic system8.76e-095
segmental subdivision of hindbrain9.15e-0912
hindbrain9.15e-0912
presumptive hindbrain9.15e-0912
occipital lobe2.28e-085
anatomical conduit2.45e-07240
diencephalon3.99e-077
future diencephalon3.99e-077
organ part5.61e-07218


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)
MA0003.16.84463
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.16.69514
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.14.83833
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.12.50216
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.13.57792
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.15.25242
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.27.08088
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.10.418966
MA0259.13.06353
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
GATA3#2625320.42738726790450.0001924415576258320.00232083185183421
REST#597849.650028716128020.0001152825614219170.00157303311109794
TAF1#687243.343046285745290.008005664898701650.0322882269301217
TBP#690843.706770687096390.005296377814784350.0244755930353214



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2733&oldid=2571244"