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Coexpression cluster:C4364: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4364_astrocytoma_Fibroblast_Smooth_Olfactory_sacrococcigeal_normal_Mesenchymal
|id=C4364
|ontology_enrichment_celltype=CL:0000055!2.60e-28!180;CL:0000057!1.01e-19!75;CL:0000192!1.39e-13!42;CL:0000514!1.39e-13!42;CL:0002321!1.44e-13!248;CL:0000220!1.78e-13!246;CL:0000393!7.43e-13!60;CL:0000211!7.43e-13!60;CL:0000680!1.10e-12!57;CL:0000056!1.10e-12!57;CL:0000355!1.10e-12!57;CL:0000187!2.42e-12!54;CL:0000183!2.62e-11!59;CL:0002620!4.32e-11!23;CL:0000359!7.60e-10!32
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!4.70e-25!365;UBERON:0003102!3.78e-22!95;UBERON:0000914!3.40e-18!83;UBERON:0002329!3.40e-18!83;UBERON:0003077!3.40e-18!83;UBERON:0003059!3.40e-18!83;UBERON:0007282!3.40e-18!83;UBERON:0009618!3.40e-18!83;UBERON:0007285!3.40e-18!83;UBERON:0000486!4.10e-16!82;UBERON:0000481!5.39e-16!347;UBERON:0000468!3.95e-14!659;UBERON:0004290!7.12e-14!70;UBERON:0002100!8.31e-14!216;UBERON:0002097!3.14e-13!40;UBERON:0005256!2.14e-12!143;UBERON:0002199!7.12e-12!45;UBERON:0002416!7.12e-12!45;UBERON:0001444!7.40e-12!48;UBERON:0003104!1.04e-11!238;UBERON:0009142!1.04e-11!238;UBERON:0000467!1.78e-11!625;UBERON:0001134!3.00e-11!61;UBERON:0002036!3.00e-11!61;UBERON:0003082!3.00e-11!61;UBERON:0000480!3.14e-11!626;UBERON:0002385!3.22e-11!63;UBERON:0001015!3.22e-11!63;UBERON:0000383!3.22e-11!63;UBERON:0004119!5.50e-10!169;UBERON:0000925!5.50e-10!169;UBERON:0006595!5.50e-10!169;UBERON:0001007!3.07e-08!155;UBERON:0001555!3.07e-08!155;UBERON:0007026!3.07e-08!155;UBERON:0000922!4.15e-08!612;UBERON:0000165!4.22e-08!28;UBERON:0000930!4.22e-08!28;UBERON:0000483!4.97e-08!309;UBERON:0000119!6.33e-08!312;UBERON:0002050!1.15e-07!605;UBERON:0005423!1.15e-07!605;UBERON:0000923!1.61e-07!604;UBERON:0005291!1.61e-07!604;UBERON:0006598!1.61e-07!604;UBERON:0002532!1.61e-07!604;UBERON:0001637!6.64e-07!42;UBERON:0003509!6.64e-07!42;UBERON:0004572!6.64e-07!42;UBERON:0000161!8.10e-07!35
}}

Latest revision as of 12:44, 17 September 2013


Full id: C4364_astrocytoma_Fibroblast_Smooth_Olfactory_sacrococcigeal_normal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr4:119274062..119274072,-p5@PRSS12
Hg19::chr4:119274086..119274113,-p4@PRSS12
Hg19::chr4:119274121..119274219,-p1@PRSS12


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>

Uber Anatomy
Ontology termp-valuen
surface structure1.23e-2199
organism subdivision1.05e-17264
multilaminar epithelium9.69e-1683
dense mesenchyme tissue1.71e-1473
somite3.33e-1471
presomitic mesoderm3.33e-1471
presumptive segmental plate3.33e-1471
dermomyotome3.33e-1471
trunk paraxial mesoderm3.33e-1471
paraxial mesoderm6.20e-1472
presumptive paraxial mesoderm6.20e-1472
multi-tissue structure1.79e-12342
epithelial vesicle2.60e-1278
skin of body3.67e-1241
multi-cellular organism7.71e-12656
skeletal muscle tissue1.15e-1162
striated muscle tissue1.15e-1162
myotome1.15e-1162
subdivision of head2.05e-1149
muscle tissue2.10e-1164
musculature2.10e-1164
musculature of body2.10e-1164
head4.61e-1156
integument7.61e-1146
integumental system7.61e-1146
anatomical system2.66e-10624
anatomical group4.20e-10625
trunk mesenchyme6.59e-10122
anterior region of body1.19e-0962
craniocervical region1.19e-0962
endoderm-derived structure1.81e-09160
endoderm1.81e-09160
presumptive endoderm1.81e-09160
trunk3.49e-09199
anatomical cluster1.63e-08373
mesenchyme3.18e-08160
entire embryonic mesenchyme3.18e-08160
mouth3.54e-0829
stomodeum3.54e-0829
unilaminar epithelium4.04e-08148
digestive system1.16e-07145
digestive tract1.16e-07145
primitive gut1.16e-07145
artery4.52e-0742
arterial blood vessel4.52e-0742
arterial system4.52e-0742
epithelium5.27e-07306
systemic artery5.32e-0733
systemic arterial system5.32e-0733
ectodermal placode5.98e-0731
cell layer6.06e-07309
orifice6.16e-0736


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.12.76432
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
MA0115.11.57693
MA0116.12.36034
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.110.1959
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.14.15415
MA0155.12.83144
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285359285133755
CTCF#1066435.360256373075030.0064925092527670.0280623752783071
CTCFL#140690319.74647435897440.0001298372005551160.00172169469131232
E2F6#187635.017155731697390.00791769806886330.0323608370294687
EBF1#187938.9064668465690.00141523283560980.00917818567550002
RAD21#5885310.35503389545630.0009004912073565420.00666712045974123
SMC3#9126315.04493284493280.0002935825420371870.0031021314354332
USF1#739136.361499277207960.00388404057290560.019090089575683
YY1#752834.911170749853860.008441455341808260.0330565112277133
ZNF143#7702313.50087655222790.0004062804962997170.00390103233916026



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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