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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.187664576755964,0

Latest revision as of 12:19, 17 September 2013


Full id: C3113_Smooth_Fibroblast_lymphangiectasia_colon_gall_mesenchymal_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr11:125462725..125462768,+p1@STT3A
Hg19::chr11:125462771..125462784,+p2@STT3A
Hg19::chr20:35807714..35807756,+p1@RPN2


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

p.valueFDRnGenesnPathwayName
2.88643650599953e-060.000913557154148851249N-Glycan biosynthesis (KEGG):00510
3.40211704163772e-050.007178466957855582167Protein processing in endoplasmic reticulum (KEGG):04141
0.0001071614097380440.01695829309104552296Metabolism of proteins (Reactome):REACT_17015
0.0002381310117449620.03014738608691222441AR up reg. targets (Netpath):NetPath_2
1.46039942267834e-060.000913557154148851235{INS,35} (Static Module):NA



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

GO IDGO nameFDR corrected p-value
GO:0018196peptidyl-asparagine modification2.70453216891284e-06
GO:0008250oligosaccharyl transferase complex2.70453216891284e-06
GO:0018279protein amino acid N-linked glycosylation via asparagine2.70453216891284e-06
GO:0004579dolichyl-diphosphooligosaccharide-protein glycotransferase activity2.70453216891284e-06
GO:0004576oligosaccharyl transferase activity2.70453216891284e-06
GO:0006487protein amino acid N-linked glycosylation2.02987218342151e-05
GO:0018193peptidyl-amino acid modification9.16662163693145e-05
GO:0006486protein amino acid glycosylation0.000145576305078965
GO:0043413biopolymer glycosylation0.000145576305078965
GO:0009101glycoprotein biosynthetic process0.000145576305078965
GO:0009100glycoprotein metabolic process0.000172974356899452
GO:0016758transferase activity, transferring hexosyl groups0.00028975026014442
GO:0016757transferase activity, transferring glycosyl groups0.000641139106386873
GO:0005789endoplasmic reticulum membrane0.000641139106386873
GO:0042175nuclear envelope-endoplasmic reticulum network0.000641139106386873
GO:0044432endoplasmic reticulum part0.00074540353528002
GO:0005783endoplasmic reticulum0.00213141778283036
GO:0012505endomembrane system0.00259198081383691
GO:0031090organelle membrane0.00530674891805402
GO:0009059macromolecule biosynthetic process0.00540140149668042
GO:0009058biosynthetic process0.0126675766612062
GO:0006464protein modification process0.0146815119011832
GO:0043412biopolymer modification0.0152200256949047
GO:0043234protein complex0.0152991783171678
GO:0016740transferase activity0.0188610573477174
GO:0032991macromolecular complex0.0256206593985365
GO:0044446intracellular organelle part0.026913961854617
GO:0044422organelle part0.026913961854617
GO:0044444cytoplasmic part0.0321256485265397
GO:0044267cellular protein metabolic process0.0455954016299721
GO:0044260cellular macromolecule metabolic process0.0455954016299721
GO:0019538protein metabolic process0.0473822131853775



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 cell9.41e-25679
eukaryotic cell9.41e-25679
somatic cell4.40e-14588
embryonic cell7.90e-14250
fibroblast4.51e-1376
native cell8.04e-12722
mesodermal cell6.31e-10121
epithelial cell8.66e-10253
non-terminally differentiated cell2.91e-09106
muscle precursor cell1.40e-0858
myoblast1.40e-0858
multi-potent skeletal muscle stem cell1.40e-0858
muscle cell5.33e-0855
smooth muscle cell1.42e-0743
smooth muscle myoblast1.42e-0743
contractile cell2.79e-0759
vascular associated smooth muscle cell4.89e-0732
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium2.48e-13148
trunk3.66e-12199
organism subdivision1.94e-11264
epithelial tube2.47e-11117
mesenchyme8.42e-11160
entire embryonic mesenchyme8.42e-11160
trunk mesenchyme2.15e-10122
splanchnic layer of lateral plate mesoderm1.44e-0883
artery2.58e-0842
arterial blood vessel2.58e-0842
arterial system2.58e-0842
vasculature6.27e-0878
vascular system6.27e-0878
vessel8.12e-0868
primordium3.16e-07160
immaterial anatomical entity4.12e-07117
systemic artery7.75e-0733
systemic arterial system7.75e-0733
Disease
Ontology termp-valuen
disease of cellular proliferation2.84e-09239
cancer3.94e-09235
ovarian cancer3.69e-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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
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
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
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
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.14.04858
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
ATF3#467214.97544968400580.005768294540793880.0259457734418352
BHLHE40#8553229.91454236465160.001467483527106140.00939396335197295
CCNT2#90536.336201576962630.003930750035764890.0189163949398788
CHD2#1106310.34402283411690.0009033701102746880.00658480394660652
E2F1#186934.907389214879320.008460985347239390.03236364081015
E2F4#1874312.66806031528440.0004917987006298980.00435463878720525
E2F6#187635.017155731697390.00791769806886330.032044815679675
ELF1#199734.258097958807540.01295179875054610.0460124127392436
EP300#203336.77394172622320.003216880500103790.016686588981342
FOS#235338.99795530889440.001372499272417130.00894883577924663
FOXA1#3169311.08141974938550.000734755275698670.00579454098306225
GABPB1#255337.067683836182170.002832212825417420.0153642985286604
IRF1#365937.63716375356390.002244692747297240.0127624511859642
IRF3#3661346.98195221148969.63568551583244e-060.000253040321747052
JUND#372736.994663941871030.002921845042734990.0156169178310235
MAX#414936.452555509007120.003721913834265510.0185764854928007
NFYA#4800318.42558069983050.0001598135507814160.0019903133114787
NFYB#4801316.75979325353650.0002123649923296180.00244965622199172
PBX3#5090321.91451268674419.49854535978121e-050.00136042043174738
RFX5#5993312.04791082719510.0005717246050312580.00483054332374885
SIN3A#2594235.408884726815140.006318961977991520.0275448086322241
SP1#666735.69838137814090.005403962701712170.0245448578152612
SP2#6668326.15353049384465.58768218891694e-050.000937615585039036
SREBF1#6720231.33723296032550.00133816265136180.00887285690721702
TAF7#6879311.43306940492390.0006690181981945830.005406344135039
USF1#739136.361499277207960.00388404057290560.0189545027519129
YY1#752834.911170749853860.008441455341808260.0327970371058782
ZEB1#6935211.25895467836260.01010222676646330.0377956819366885



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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