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Coexpression cluster:C3515: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3515_neuroblastoma_neuroectodermal_brain_pineal_Retinal_Mesothelial_amygdala
|id=C3515
}}

Latest revision as of 12:27, 17 September 2013


Full id: C3515_neuroblastoma_neuroectodermal_brain_pineal_Retinal_Mesothelial_amygdala



Phase1 CAGE Peaks

Hg19::chr15:77363355..77363369,-p3@TSPAN3
Hg19::chr15:77363375..77363406,-p2@TSPAN3
Hg19::chr15:77363411..77363423,-p4@TSPAN3


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 system5.84e-2889
central nervous system7.61e-2681
brain2.73e-2368
future brain2.73e-2368
neural tube2.01e-2056
neural rod2.01e-2056
future spinal cord2.01e-2056
neural keel2.01e-2056
anatomical cluster4.75e-20373
neurectoderm8.31e-2086
regional part of nervous system5.57e-1953
regional part of brain5.57e-1953
neural plate5.66e-1982
presumptive neural plate5.66e-1982
ectoderm-derived structure2.57e-17171
ectoderm2.57e-17171
presumptive ectoderm2.57e-17171
structure with developmental contribution from neural crest1.41e-16132
regional part of forebrain3.22e-1641
forebrain3.22e-1641
anterior neural tube3.22e-1641
future forebrain3.22e-1641
pre-chordal neural plate1.06e-1561
ecto-epithelium6.89e-15104
cell layer2.01e-14309
tube2.13e-14192
epithelium2.73e-14306
telencephalon3.08e-1334
brain grey matter3.71e-1334
gray matter3.71e-1334
anatomical conduit7.10e-13240
cerebral hemisphere8.67e-1332
regional part of telencephalon2.09e-1232
organ system subdivision5.97e-12223
cerebral cortex1.00e-0925
pallium1.00e-0925
regional part of cerebral cortex2.89e-0922
multi-tissue structure1.83e-08342
neocortex1.91e-0820


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)
MA0003.11.0927
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.16.20416
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.12.83144
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
E2F1#186934.907389214879320.008460985347239390.0324623213210512
E2F6#187635.017155731697390.00791769806886330.0321457187301358
EBF1#187938.9064668465690.00141523283560980.00914015843907318
HMGN3#932438.178547723350590.001827766942164210.0108552830066925
IRF1#365937.63716375356390.002244692747297240.0127847230100331
MAX#414936.452555509007120.003721913834265510.0186236565224634
MXI1#460139.96157162875930.001011470541259020.00719401878633553
NFYA#4800318.42558069983050.0001598135507814160.00199316544423935
NFYB#4801316.75979325353650.0002123649923296180.00245453601526262
NRF1#4899312.21027944771090.0005492172401020010.00470469974893478
RFX5#5993312.04791082719510.0005717246050312580.00483994050618947
SMARCB1#6598318.25271578115740.000164397760679890.00202805784640291
SP1#666735.69838137814090.005403962701712170.0246026355973896
SP2#6668326.15353049384465.58768218891694e-050.000939124461101216
TFAP2A#7020316.5186343730450.0002218033880766340.00247859234403334
TFAP2C#7022310.80922860986020.0007916746575753130.00614414130656967
USF1#739136.361499277207960.00388404057290560.0189980008146163
YY1#752834.911170749853860.008441455341808260.0328679549059804
ZBTB7A#5134137.35190930787590.002516255860282270.0139888877777078
ZNF263#1012738.221841637010680.001799043925565870.010918778971535



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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