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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.017073769275719,0

Latest revision as of 12:08, 17 September 2013


Full id: C2545_skeletal_Mast_Mesenchymal_stomach_lung_left_rectum



Phase1 CAGE Peaks

Hg19::chr1:184356112..184356185,+p1@C1orf21
Hg19::chr1:184356188..184356200,+p3@C1orf21
Hg19::chr1:184356231..184356262,+p2@C1orf21
Hg19::chr1:184356271..184356286,+p4@C1orf21


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
adult organism2.08e-30114
neural tube8.49e-2156
neural rod8.49e-2156
future spinal cord8.49e-2156
neural keel8.49e-2156
regional part of nervous system1.43e-1953
regional part of brain1.43e-1953
ectoderm-derived structure8.45e-19171
ectoderm8.45e-19171
presumptive ectoderm8.45e-19171
neural plate4.96e-1882
presumptive neural plate4.96e-1882
ecto-epithelium1.03e-17104
neurectoderm5.75e-1786
regional part of forebrain6.96e-1741
forebrain6.96e-1741
anterior neural tube6.96e-1741
future forebrain6.96e-1741
nervous system2.13e-1689
structure with developmental contribution from neural crest2.77e-16132
central nervous system2.92e-1681
brain grey matter7.69e-1634
gray matter7.69e-1634
brain7.99e-1668
future brain7.99e-1668
telencephalon1.09e-1534
cerebral hemisphere2.34e-1532
regional part of telencephalon4.60e-1532
regional part of cerebral cortex1.32e-1322
cerebral cortex5.75e-1325
pallium5.75e-1325
pre-chordal neural plate1.51e-1261
neocortex1.83e-1220
organ system subdivision5.01e-12223
anatomical cluster1.71e-11373
multi-cellular organism3.22e-11656
multi-tissue structure1.43e-10342
anatomical group4.99e-10625
anatomical system8.08e-10624
embryonic structure1.34e-09564
anatomical conduit2.33e-09240
germ layer5.55e-09560
germ layer / neural crest5.55e-09560
embryonic tissue5.55e-09560
presumptive structure5.55e-09560
germ layer / neural crest derived structure5.55e-09560
epiblast (generic)5.55e-09560
epithelium1.08e-08306
cell layer2.05e-08309
developing anatomical structure2.66e-07581
organ part3.28e-07218
organ3.46e-07503


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.14.03238
MA0009.11.20602
MA0014.12.45009
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
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.12.54366
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.13.20115
MA0069.12.67291
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.112.0849
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.12.05499
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
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
MA0146.12.31379
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.24.29465
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.12.59564
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.13.48623
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.12.49771
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.29.97441
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
CCNT2#90546.336201576962630.0006203100587215640.00512373949879955
E2F1#186944.907389214879320.001724022357361790.0106516310329217
EGR1#195844.988179094810140.001615011500076050.0101480167292247
MYC#460945.22228187160940.001344309395272740.00887978805470175
RAD21#5885410.35503389545638.6948481184721e-050.0012944850215896
ZBTB7A#5134147.35190930787590.000342223540015990.00346735392857295
ZNF263#1012748.221841637010680.0002187871180958320.00248991040937241



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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