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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.039752169124133,

Latest revision as of 12:23, 17 September 2013


Full id: C3324_Smooth_Tracheal_mucinous_Bronchial_chronic_iPS_testicular



Phase1 CAGE Peaks

Hg19::chr12:6978028..6978039,+p3@TPI1
Hg19::chr1:8927211..8927246,-p@chr1:8927211..8927246
-
Hg19::chr1:8934931..8934947,-p4@ENO1


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
5.10526184734612e-060.00161581537468505265Glycolysis / Gluconeogenesis (KEGG):00010
2.76862277106078e-060.00161581537468505248Glycolysis and Gluconeogenesis (Wikipathways):WP534
1.93288158883898e-050.004078380152450252126Metabolism of carbohydrates (Reactome):REACT_474



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:0006096glycolysis0.000540199366548864
GO:0006007glucose catabolic process0.000540199366548864
GO:0019320hexose catabolic process0.000540199366548864
GO:0046365monosaccharide catabolic process0.000540199366548864
GO:0046164alcohol catabolic process0.000540199366548864
GO:0044275cellular carbohydrate catabolic process0.000540199366548864
GO:0016052carbohydrate catabolic process0.000540199366548864
GO:0006006glucose metabolic process0.000540199366548864
GO:0019682glyceraldehyde-3-phosphate metabolic process0.000801364291142872
GO:0019318hexose metabolic process0.000801364291142872
GO:0005996monosaccharide metabolic process0.000801364291142872
GO:0006066alcohol metabolic process0.00194031033381917
GO:0044262cellular carbohydrate metabolic process0.00222563009254727
GO:0044265cellular macromolecule catabolic process0.00229801901433619
GO:0008243plasminogen activator activity0.0026687074290719
GO:0009057macromolecule catabolic process0.00287246063691723
GO:0004807triose-phosphate isomerase activity0.00381215860215283
GO:0005975carbohydrate metabolic process0.00381215860215283
GO:0044248cellular catabolic process0.00381215860215283
GO:0000015phosphopyruvate hydratase complex0.00381215860215283
GO:0004634phosphopyruvate hydratase activity0.00381215860215283
GO:0006098pentose-phosphate shunt0.00452466669138058
GO:0006740NADPH regeneration0.00452466669138058
GO:0009056catabolic process0.00464384082415092
GO:0006739NADP metabolic process0.00544320154386884
GO:0006081aldehyde metabolic process0.00738819991474676
GO:0006094gluconeogenesis0.00741089388558953
GO:0016861intramolecular oxidoreductase activity, interconverting aldoses and ketoses0.00771768936066741
GO:0006090pyruvate metabolic process0.00800329401828087
GO:0006769nicotinamide metabolic process0.0088031049041376
GO:0019319hexose biosynthetic process0.00894367264301036
GO:0046165alcohol biosynthetic process0.00894367264301036
GO:0019362pyridine nucleotide metabolic process0.00894367264301036
GO:0046364monosaccharide biosynthetic process0.00894367264301036
GO:0006733oxidoreduction coenzyme metabolic process0.0114297418328042
GO:0030308negative regulation of cell growth0.0116761834286374
GO:0045792negative regulation of cell size0.0116761834286374
GO:0045926negative regulation of growth0.0128413395414501
GO:0006767water-soluble vitamin metabolic process0.0131268421898135
GO:0016860intramolecular oxidoreductase activity0.0137975509083469
GO:0006633fatty acid biosynthetic process0.0142405352847658
GO:0046394carboxylic acid biosynthetic process0.0154359354486916
GO:0016053organic acid biosynthetic process0.0154359354486916
GO:0006766vitamin metabolic process0.0156296729918687
GO:0016836hydro-lyase activity0.0159922110028098
GO:0016835carbon-oxygen lyase activity0.0175538202251983
GO:0003714transcription corepressor activity0.0181993389241271
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0211448259831228
GO:0016051carbohydrate biosynthetic process0.0225037134075076
GO:0001558regulation of cell growth0.0258798910505056
GO:0044445cytosolic part0.0293265925339893
GO:0006631fatty acid metabolic process0.0293265925339893
GO:0016049cell growth0.0293639592890473
GO:0040008regulation of growth0.0293639592890473
GO:0045892negative regulation of transcription, DNA-dependent0.0293639592890473
GO:0008361regulation of cell size0.0293639592890473
GO:0016564transcription repressor activity0.0299656044669309
GO:0016829lyase activity0.0380323582947717
GO:0032787monocarboxylic acid metabolic process0.0380323582947717
GO:0006732coenzyme metabolic process0.0380323582947717
GO:0016481negative regulation of transcription0.0380323582947717
GO:0003712transcription cofactor activity0.0388270803655245
GO:0016853isomerase activity0.0397210780239578
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0397210780239578
GO:0008610lipid biosynthetic process0.0401829081725927
GO:0004252serine-type endopeptidase activity0.0401829081725927
GO:0009117nucleotide metabolic process0.0401829081725927
GO:0051186cofactor metabolic process0.0401829081725927
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.042131259085518
GO:0008236serine-type peptidase activity0.042131259085518
GO:0017171serine hydrolase activity0.042131259085518
GO:0031324negative regulation of cellular metabolic process0.042131259085518
GO:0006357regulation of transcription from RNA polymerase II promoter0.0461062077148254
GO:0008134transcription factor binding0.0462469925712618
GO:0009892negative regulation of metabolic process0.0462469925712618
GO:0000287magnesium ion binding0.0467822848085108
GO:0000902cell morphogenesis0.0487215706423031
GO:0032989cellular structure morphogenesis0.0487215706423031



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
artery5.36e-1142
arterial blood vessel5.36e-1142
arterial system5.36e-1142
epithelial vesicle1.39e-1078
unilaminar epithelium1.85e-09148
dense mesenchyme tissue3.31e-0973
somite3.50e-0971
presomitic mesoderm3.50e-0971
presumptive segmental plate3.50e-0971
dermomyotome3.50e-0971
trunk paraxial mesoderm3.50e-0971
paraxial mesoderm3.73e-0972
presumptive paraxial mesoderm3.73e-0972
epithelial tube open at both ends5.11e-0959
blood vessel5.11e-0959
blood vasculature5.11e-0959
vascular cord5.11e-0959
epithelial tube5.18e-09117
multilaminar epithelium2.55e-0883
vessel4.57e-0868
vasculature9.04e-0878
vascular system9.04e-0878
splanchnic layer of lateral plate mesoderm9.23e-0883
systemic artery1.27e-0733
systemic arterial system1.27e-0733
trunk mesenchyme2.87e-07122
skeletal muscle tissue5.44e-0762
striated muscle tissue5.44e-0762
myotome5.44e-0762


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
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
MA0088.11.31954
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
MA0105.12.3269
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
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
MA0145.10.752137
MA0146.10.107247
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
MA0065.20.760954
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
MA0162.10.149099
MA0163.10.387745
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

No analysis results for this cluster

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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