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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.225338062286747,

Latest revision as of 12:07, 17 September 2013


Full id: C2540_small_neuroblastoma_nonsmall_Urothelial_colon_anaplastic_Smooth



Phase1 CAGE Peaks

Hg19::chr1:165796753..165796776,+p5@UCK2
Hg19::chr1:165796782..165796803,+p2@UCK2
Hg19::chr1:165796811..165796860,+p1@UCK2
Hg19::chr1:165796870..165796886,+p4@UCK2


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 cell7.98e-33253
animal cell8.38e-23679
eukaryotic cell8.38e-23679
embryonic cell2.29e-22250
squamous epithelial cell8.98e-1163
native cell2.12e-10722
mesodermal cell1.09e-08121
endo-epithelial cell2.04e-0842
endodermal cell8.53e-0858
Uber Anatomy
Ontology termp-valuen
organism subdivision2.75e-10264
trunk4.24e-09199
endoderm-derived structure1.10e-08160
endoderm1.10e-08160
presumptive endoderm1.10e-08160
unilaminar epithelium2.93e-08148
cell layer5.76e-08309
mesenchyme1.02e-07160
entire embryonic mesenchyme1.02e-07160
respiratory primordium1.77e-0738
endoderm of foregut1.77e-0738
epithelium1.79e-07306
segment of respiratory tract2.11e-0747
larynx2.43e-079
epithelial tube2.70e-07117
respiratory system2.99e-0774
multilaminar epithelium5.74e-0783
surface structure8.71e-0799
respiratory tract9.51e-0754
Disease
Ontology termp-valuen
cancer2.40e-28235
disease of cellular proliferation7.57e-28239
cell type cancer5.82e-18143
carcinoma7.35e-15106
organ system cancer3.79e-11137


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
MA0014.10.244769
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.69331
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
MA0088.10.182167
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
MA0113.13.3942
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
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
MA0144.10.430413
MA0145.10.569905
MA0146.12.31379
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.21.09513
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
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.80246
MA0163.10.918944
MA0164.16.48408
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.5408
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#90546.336201576962630.0006203100587215640.00512333429994634
CTCF#1066445.360256373075030.001211145381643620.00817599460367645
CTCFL#140690419.74647435897446.5732084880439e-060.000192999528052521
E2F1#186944.907389214879320.001724022357361790.0106510009453125
E2F6#187645.017155731697390.00157802193473060.00997138388439793
EGR1#195844.988179094810140.001615011500076050.0101474062120348
ELF1#199744.258097958807540.003041525565781240.0160951504136921
GABPB1#255347.067683836182170.0004006876864423170.00390367735861466
HEY1#2346244.040111043105710.00375304636917980.0186162151389584
NFYA#4800418.42558069983058.67100748407158e-060.000234548394361293
NFYB#4801416.75979325353651.26678572070404e-050.000311518327959994
NR2C2#7182432.61461090524098.82887529809196e-073.81971378317078e-05
SMARCB1#6598418.25271578115749.00423392720929e-060.000241560027517033
TAF1#687243.343046285745290.008005664898701650.0322396713332113
TAF7#6879411.43306940492395.85061525419808e-050.000969584904051402
TAL1#6886214.93430833872010.006428077577888070.0279492920131995
TBP#690843.706770687096390.005296377814784350.0244366673704834
USF1#739146.361499277207960.0006105011399140830.00508129809941719



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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