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Coexpression cluster:C2888: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2888_clear_Fibroblast_papillotubular_transitionalcell_malignant_schwannoma_squamous
|id=C2888
|ontology_enrichment_celltype=CL:0000548!2.48e-19!679;CL:0000004!2.48e-19!679;CL:0000255!2.48e-19!679;CL:0000012!2.77e-19!682;CL:0000220!2.83e-17!246;CL:0002321!3.70e-17!248;CL:0000066!2.24e-14!254;CL:0000055!1.61e-13!180;CL:0000144!7.16e-13!625;CL:0002371!3.40e-11!591;CL:0000003!5.13e-11!722;CL:0000063!5.49e-10!578;CL:0000222!3.94e-08!119;CL:0000359!2.43e-07!32;CL:0000076!2.69e-07!62
|ontology_enrichment_disease=DOID:2394!2.95e-07!14;DOID:1749!9.06e-07!14
|ontology_enrichment_uberon=UBERON:0002049!1.76e-09!79;UBERON:0007798!1.76e-09!79;UBERON:0000055!1.28e-08!69;UBERON:0000467!2.54e-07!625;UBERON:0000480!2.69e-07!626;UBERON:0002097!4.14e-07!40;UBERON:0000468!5.57e-07!659;UBERON:0001637!7.39e-07!42;UBERON:0003509!7.39e-07!42;UBERON:0004572!7.39e-07!42;UBERON:0003102!9.10e-07!95
}}

Latest revision as of 12:15, 17 September 2013


Full id: C2888_clear_Fibroblast_papillotubular_transitionalcell_malignant_schwannoma_squamous



Phase1 CAGE Peaks

Hg19::chr7:18548878..18548909,+p4@HDAC9
Hg19::chr7:18548912..18548923,+p11@HDAC9
Hg19::chr7:18548924..18548947,+p5@HDAC9
Hg19::chr7:18548958..18549006,+p2@HDAC9


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
animal cell1.23e-18679
eukaryotic cell1.23e-18679
embryonic cell1.71e-16250
epithelial cell2.34e-14253
somatic cell2.51e-11588
native cell5.80e-11722
mesodermal cell5.58e-08121
non-terminally differentiated cell6.13e-08106
squamous epithelial cell1.99e-0763
Uber Anatomy
Ontology termp-valuen
vasculature7.20e-0978
vascular system7.20e-0978
vessel6.78e-0868
anatomical system2.20e-07624
multi-cellular organism2.50e-07656
anatomical group2.52e-07625
surface structure2.62e-0799
organism subdivision4.47e-07264
skin of body6.13e-0741
Disease
Ontology termp-valuen
ovarian cancer1.94e-0714
squamous cell carcinoma9.67e-0714


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
MA0014.10.0695829
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
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.13.49299
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.16.00922
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
MA0101.13.36866
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.12.98058
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
MA0122.12.8366
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.13.22431
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
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
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.23.3522
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
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
EP300#203346.77394172622320.0004748459821442640.00435326891934382
FOS#235348.99795530889440.0001525147711168630.00195441597308884
GATA2#2624412.7449317335543.78864877853583e-050.000724560867572796
GATA3#2625427.2365163572061.81561517799785e-066.79401768451871e-05
JUN#3725412.51282919233634.07770316866756e-050.000745051156809782
NFKB1#479045.488063424193840.001102199566301980.00769315113981236
STAT3#6774410.51946499715428.16377768286615e-050.00123513947185406



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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