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Coexpression cluster:C2734: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2734_occipital_locus_brain_amygdala_cerebellum_temporal_postcentral
|id=C2734
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:0050687!5.24e-14!143;DOID:305!1.28e-12!106;DOID:14566!1.84e-12!239;DOID:162!9.31e-12!235
|ontology_enrichment_uberon=UBERON:0005743!3.21e-32!86;UBERON:0000073!4.20e-32!94;UBERON:0001016!4.20e-32!94;UBERON:0001017!8.22e-32!82;UBERON:0001049!3.00e-27!57;UBERON:0005068!3.00e-27!57;UBERON:0006241!3.00e-27!57;UBERON:0007135!3.00e-27!57;UBERON:0000955!5.76e-26!69;UBERON:0006238!5.76e-26!69;UBERON:0002616!1.27e-22!59;UBERON:0003075!5.38e-22!86;UBERON:0007284!5.38e-22!86;UBERON:0002780!1.08e-21!41;UBERON:0001890!1.08e-21!41;UBERON:0006240!1.08e-21!41;UBERON:0002346!1.36e-20!90;UBERON:0003080!1.84e-20!42;UBERON:0002020!1.06e-19!34;UBERON:0003528!1.06e-19!34;UBERON:0001893!2.21e-19!34;UBERON:0002791!9.35e-19!33;UBERON:0001869!1.61e-18!32;UBERON:0004121!2.48e-18!169;UBERON:0000924!1.28e-17!173;UBERON:0006601!1.28e-17!173;UBERON:0003056!7.59e-17!61;UBERON:0000033!2.12e-16!123;UBERON:0002619!2.68e-15!22;UBERON:0000956!1.35e-14!25;UBERON:0000203!1.35e-14!25;UBERON:0000153!1.71e-14!129;UBERON:0007811!1.71e-14!129;UBERON:0001950!3.88e-14!20;UBERON:0000025!4.71e-13!194;UBERON:0000475!5.08e-11!365;UBERON:0000483!2.69e-10!309;UBERON:0000481!2.97e-10!347;UBERON:0000119!3.43e-10!312;UBERON:0000477!1.27e-09!286;UBERON:0004111!2.51e-09!241;UBERON:0000064!1.29e-08!219;UBERON:0003076!6.14e-08!15;UBERON:0003057!6.14e-08!15;UBERON:0000922!8.94e-07!612
}}

Latest revision as of 12:11, 17 September 2013


Full id: C2734_occipital_locus_brain_amygdala_cerebellum_temporal_postcentral



Phase1 CAGE Peaks

Hg19::chr3:183979256..183979300,-p2@CAMK2N2
Hg19::chr3:183979335..183979351,-p4@CAMK2N2
Hg19::chr3:183979353..183979390,-p3@CAMK2N2
Hg19::chr3:183979460..183979484,-p5@CAMK2N2


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>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell4.68e-07253
Uber Anatomy
Ontology termp-valuen
central nervous system1.20e-3181
nervous system2.70e-3189
neural tube7.42e-2756
neural rod7.42e-2756
future spinal cord7.42e-2756
neural keel7.42e-2756
brain1.35e-2568
future brain1.35e-2568
regional part of nervous system5.24e-2553
regional part of brain5.24e-2553
neural plate3.24e-2182
presumptive neural plate3.24e-2182
regional part of forebrain7.31e-2141
forebrain7.31e-2141
anterior neural tube7.31e-2141
future forebrain7.31e-2141
brain grey matter4.90e-2034
gray matter4.90e-2034
neurectoderm7.00e-2086
telencephalon1.19e-1934
cerebral hemisphere8.41e-1932
regional part of telencephalon1.27e-1832
pre-chordal neural plate1.06e-1761
ecto-epithelium2.65e-17104
ectoderm-derived structure3.85e-16171
ectoderm3.85e-16171
presumptive ectoderm3.85e-16171
organ system subdivision4.53e-16223
regional part of cerebral cortex1.33e-1522
structure with developmental contribution from neural crest2.96e-15132
cerebral cortex8.08e-1525
pallium8.08e-1525
neocortex2.15e-1420
anatomical cluster9.61e-13373
tube9.98e-12192
multi-tissue structure5.37e-10342
epithelium3.86e-09306
cell layer5.04e-09309
anatomical conduit2.98e-08240
organ part1.05e-07218
posterior neural tube3.33e-0715
chordal neural plate3.33e-0715
Disease
Ontology termp-valuen
cell type cancer1.10e-14143
carcinoma1.97e-13106
disease of cellular proliferation6.72e-13239
cancer3.47e-12235


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)
MA0003.11.05935
MA0004.12.8475
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.13.76953
MA0017.10.577281
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.11.28333
MA0058.12.50688
MA0059.12.50216
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.125.6365
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.14.51906
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.01976
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
MA0145.10.195821
MA0146.11.75643
MA0147.13.01834
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.210.3536
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.22.6968
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.13.05999
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.111.5378
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.223.997
MA0102.21.75932
MA0258.10.418966
MA0259.12.06681
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#186944.907389214879320.001724022357361790.0106661436514725
E2F6#187645.017155731697390.00157802193473060.00998225516906899
GABPB1#255335.300762877136630.01012678824234270.0378740067051757
JUND#372735.245997956403270.01043432751748420.0387067816863868
MAX#414946.452555509007120.0005767613195645490.00485973178329987
MXI1#460149.96157162875930.0001015224754950450.0014260801369505
MYC#460945.22228187160940.001344309395272740.0088876577155719
REST#597849.650028716128020.0001152825614219170.00157323865573548
SMARCC1#6599332.74751948972364.71941722862287e-050.000825060622598165
USF1#739146.361499277207960.0006105011399140830.00508616213716392
USF2#7392412.99219738506963.50833029870167e-050.000682321244070956



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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