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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 12:13, 17 September 2013


Full id: C2800_pineal_teratocarcinoma_hepatoblastoma_optic_testicular_spinal_H9



Phase1 CAGE Peaks

Hg19::chr5:115808548..115808552,-p@chr5:115808548..115808552
-
Hg19::chr5:115910459..115910474,-p2@SEMA6A
Hg19::chr5:115910475..115910491,-p3@SEMA6A
Hg19::chr5:115910498..115910536,-p1@SEMA6A


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><br>

Cell Type
Ontology termp-valuen
melanocyte1.99e-0710
melanoblast1.99e-0710
Uber Anatomy
Ontology termp-valuen
adult organism3.54e-34114
central nervous system1.65e-3381
nervous system1.28e-3289
neural tube1.77e-3056
neural rod1.77e-3056
future spinal cord1.77e-3056
neural keel1.77e-3056
regional part of nervous system2.01e-2853
regional part of brain2.01e-2853
brain2.40e-2668
future brain2.40e-2668
neurectoderm2.93e-2586
organ system subdivision3.89e-25223
neural plate3.32e-2482
presumptive neural plate3.32e-2482
anatomical cluster3.82e-23373
regional part of forebrain1.06e-2241
forebrain1.06e-2241
anterior neural tube1.06e-2241
future forebrain1.06e-2241
ectoderm-derived structure2.07e-22171
ectoderm2.07e-22171
presumptive ectoderm2.07e-22171
ecto-epithelium2.60e-20104
brain grey matter1.28e-1934
gray matter1.28e-1934
telencephalon1.82e-1934
regional part of telencephalon2.47e-1832
cerebral hemisphere3.95e-1832
pre-chordal neural plate8.52e-1761
anatomical conduit2.84e-16240
structure with developmental contribution from neural crest5.79e-16132
tube4.05e-15192
cerebral cortex2.23e-1425
pallium2.23e-1425
multi-tissue structure9.62e-14342
regional part of cerebral cortex2.28e-1322
neocortex2.90e-1220
cell layer4.41e-12309
epithelium5.18e-12306
multi-cellular organism7.94e-11656
embryo3.22e-10592
posterior neural tube7.11e-0915
chordal neural plate7.11e-0915
organ part9.83e-09218
developing anatomical structure2.00e-08581
anatomical group7.71e-08625
organ1.01e-07503
anatomical system1.09e-07624
segmental subdivision of nervous system1.20e-0713
segmental subdivision of hindbrain5.92e-0712
hindbrain5.92e-0712
presumptive hindbrain5.92e-0712


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
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
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
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
MA0088.11.02755
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
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.12.76745
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0270533
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
BCLAF1#9774316.23948570759140.000380256706766480.00376718176797423
CTBP2#1488347.03775025449611.60047699357395e-050.000370379385623466
EBF1#187936.679850134926750.005184294118278910.0240598335148832
EP300#203335.08045629466740.01144298405398240.041912527586935
IRF4#3662316.43588451505810.0003669431395554610.00365993453844263
JUND#372735.245997956403270.01043432751748420.0387109065965164
NANOG#79923321.93358386075950.0001557535816382770.00196529519303129
PAX5#507935.002174148383370.01196533174786410.0435174565543661
POU2F2#545236.829593043306890.004860473775203740.0227725548700598
RAD21#588537.766275421592250.0033411193858720.0172735591080187
REST#597837.237521537096020.004104697304192610.0195892196011959
RFX5#599339.035933120396320.002144561191324070.0123880434878703
TAF7#687938.574802053692940.00250055433515240.0140383483421481
TCF12#693837.975848676639820.003090920396013070.0162872167123718
TCF7L2#693438.077632422353010.002978381685834620.0158671294065947
TRIM28#10155313.94289378394690.0005972858184258420.00499639035567292
USF1#739134.771124457905970.01370465887188020.0483270036776274
ZEB1#6935312.66632401315790.000793336075912850.00613515190168546
ZNF263#1012736.166381227758010.006539814347975980.0279876934391191



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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