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Coexpression cluster:C2946: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2946_large_tubular_gastric_papillary_embryonic_small_cervical
|id=C2946
}}

Latest revision as of 12:16, 17 September 2013


Full id: C2946_large_tubular_gastric_papillary_embryonic_small_cervical



Phase1 CAGE Peaks

Hg19::chr9:74764278..74764289,+p4@GDA
Hg19::chr9:74764317..74764339,+p2@GDA
Hg19::chr9:74764340..74764392,+p1@GDA
Hg19::chr9:74764397..74764408,+p3@GDA


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
regional part of forebrain8.38e-2641
forebrain8.38e-2641
anterior neural tube8.38e-2641
future forebrain8.38e-2641
adult organism4.54e-25114
telencephalon6.78e-2534
brain grey matter3.15e-2434
gray matter3.15e-2434
organ system subdivision7.20e-24223
cerebral hemisphere7.95e-2432
regional part of cerebral cortex1.41e-2322
regional part of telencephalon2.98e-2332
neural tube1.10e-2256
neural rod1.10e-2256
future spinal cord1.10e-2256
neural keel1.10e-2256
regional part of nervous system2.04e-2253
regional part of brain2.04e-2253
neocortex1.76e-2120
cerebral cortex1.01e-1925
pallium1.01e-1925
brain3.14e-1768
future brain3.14e-1768
pre-chordal neural plate1.33e-1561
central nervous system2.02e-1581
neurectoderm1.67e-1486
nervous system1.76e-1489
neural plate1.39e-1382
presumptive neural plate1.39e-1382
organ5.11e-13503
anatomical cluster5.74e-13373
multi-tissue structure3.68e-12342
organ part8.59e-12218
subdivision of digestive tract1.10e-10118
ecto-epithelium6.99e-10104
larynx1.76e-099
endoderm-derived structure1.93e-09160
endoderm1.93e-09160
presumptive endoderm1.93e-09160
digestive system2.52e-09145
digestive tract2.52e-09145
primitive gut2.52e-09145
structure with developmental contribution from neural crest4.85e-09132
embryo6.87e-09592
tube1.03e-08192
temporal lobe3.04e-086
multi-cellular organism9.59e-08656
ectoderm-derived structure1.57e-07171
ectoderm1.57e-07171
presumptive ectoderm1.57e-07171
gyrus1.93e-076
anatomical system2.26e-07624
developing anatomical structure2.32e-07581
anatomical group2.75e-07625
upper respiratory tract2.83e-0719
gastrointestinal system2.91e-0725
anatomical conduit3.93e-07240
basal ganglion3.98e-079
nuclear complex of neuraxis3.98e-079
aggregate regional part of brain3.98e-079
collection of basal ganglia3.98e-079
cerebral subcortex3.98e-079
intestine4.04e-0717
foregut5.10e-0787
respiratory tract6.33e-0754
limbic system7.38e-075
respiratory primordium9.78e-0738
endoderm of foregut9.78e-0738
Disease
Ontology termp-valuen
carcinoma1.75e-13106
adenocarcinoma7.39e-1225
cell type cancer4.84e-08143


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)
MA0003.11.8989
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.13.53539
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
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
MA0048.14.64626
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
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
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.13.24733
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.11.13665
MA0115.13.20374
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.12.92476
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.23.60805
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.21.05083
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.13.02177
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
CEBPB#105147.971147625824820.0002476385788090830.00268903363820355
E2F1#186944.907389214879320.001724022357361790.0106889386156431
TAF1#687243.343046285745290.008005664898701650.032354447657128
TBP#690843.706770687096390.005296377814784350.0245200763596907



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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