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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:16, 17 September 2013


Full id: C2956_endometrial_nonsmall_cholangiocellular_liposarcoma_lymphangiectasia_medulloblastoma_melanoma



Phase1 CAGE Peaks

Hg19::chrX:151903196..151903211,-p1@MAGEA12
Hg19::chrX:151903207..151903234,+p1@CSAG1
Hg19::chrX:151903235..151903247,+p3@CSAG1
Hg19::chrX:151903253..151903273,+p2@CSAG1


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
neural tube3.28e-1856
neural rod3.28e-1856
future spinal cord3.28e-1856
neural keel3.28e-1856
brain3.43e-1868
future brain3.43e-1868
central nervous system5.59e-1881
nervous system3.55e-1789
regional part of nervous system6.34e-1753
regional part of brain6.34e-1753
larynx2.00e-159
brain grey matter2.15e-1434
gray matter2.15e-1434
telencephalon3.09e-1434
regional part of forebrain2.17e-1341
forebrain2.17e-1341
anterior neural tube2.17e-1341
future forebrain2.17e-1341
organ system subdivision7.90e-13223
regional part of telencephalon1.53e-1232
regional part of cerebral cortex1.55e-1222
cerebral hemisphere1.92e-1232
neocortex2.23e-1220
cerebral cortex4.09e-1225
pallium4.09e-1225
neural plate7.90e-1082
presumptive neural plate7.90e-1082
neurectoderm5.14e-0986
ecto-epithelium2.82e-08104
respiratory primordium3.18e-0838
endoderm of foregut3.18e-0838
pre-chordal neural plate3.54e-0761
adult organism8.54e-07114
Disease
Ontology termp-valuen
cancer5.83e-21235
disease of cellular proliferation7.79e-21239
cell type cancer5.17e-18143
carcinoma2.27e-12106
organ system cancer5.62e-09137


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.11.47358
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.13.36035
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.11.8408
MA0072.11.1744
MA0073.111.2932
MA0074.10.819248
MA0076.12.5647
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
MA0100.13.24733
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
MA0114.10.447443
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
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.11.92815
MA0145.10.569905
MA0146.12.92476
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
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
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.24.78886
MA0099.20.7872
MA0079.20.657636
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
CHD2#1106410.34402283411698.73193255208051e-050.00129428655096045
E2F6#187645.017155731697390.00157802193473060.0099998199648886
ELF1#199744.258097958807540.003041525565781240.01613521047212
ETS1#211349.728760922202340.0001115955317418140.0015492390987084
GABPB1#255347.067683836182170.0004006876864423170.00391133949755576
HEY1#2346244.040111043105710.00375304636917980.0186738642091839
TAF1#687243.343046285745290.008005664898701650.0323582041238245
TBP#690843.706770687096390.005296377814784350.0245244248547224
USF1#739146.361499277207960.0006105011399140830.00509428959343935
YY1#752844.911170749853860.00171871838055440.0107152118521204
ZBTB33#10009431.66472502998129.93721537730495e-074.21027519996086e-05



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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