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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.145065619270062,

Latest revision as of 14:21, 17 September 2013


Full id: C4862_Neutrophils_large_meningioma_Pericytes_leiomyoma_Nucleus_Dendritic



Phase1 CAGE Peaks

Hg19::chrX:153761003..153761024,-p4@G6PD
Hg19::chrX:153763451..153763480,-p1@M12996
Hg19::chrX:153764189..153764228,-p@chrX:153764189..153764228
-


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

GO IDGO nameFDR corrected p-value
GO:0006010glucose 6-phosphate utilization0.00123631225715295
GO:0051156glucose 6-phosphate metabolic process0.00123631225715295
GO:0004345glucose-6-phosphate dehydrogenase activity0.0024726245143059
GO:0006740NADPH regeneration0.00321441186859767
GO:0006098pentose-phosphate shunt0.00321441186859767
GO:0006739NADP metabolic process0.00350288472860002
GO:0006769nicotinamide metabolic process0.00582832921229247
GO:0019362pyridine nucleotide metabolic process0.00587248322147651
GO:0006733oxidoreduction coenzyme metabolic process0.0068684014286275
GO:0006767water-soluble vitamin metabolic process0.00791239844577887
GO:0006766vitamin metabolic process0.00966571401046851
GO:0006007glucose catabolic process0.0118685976686683
GO:0019320hexose catabolic process0.0118685976686683
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0118685976686683
GO:0046365monosaccharide catabolic process0.0118685976686683
GO:0046164alcohol catabolic process0.0118685976686683
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0118685976686683
GO:0044275cellular carbohydrate catabolic process0.0118685976686683
GO:0016052carbohydrate catabolic process0.0118685976686683
GO:0006006glucose metabolic process0.0118685976686683
GO:0019318hexose metabolic process0.0153977072027231
GO:0005996monosaccharide metabolic process0.0153977072027231
GO:0006732coenzyme metabolic process0.0154807795678282
GO:0009117nucleotide metabolic process0.0169622041681385
GO:0051186cofactor metabolic process0.0169622041681385
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0174510230144282
GO:0006066alcohol metabolic process0.0203762575715949
GO:0044262cellular carbohydrate metabolic process0.0219003885552808
GO:0044265cellular macromolecule catabolic process0.0222962520858963
GO:0009057macromolecule catabolic process0.0257565053573531
GO:0005975carbohydrate metabolic process0.031255519251148
GO:0044248cellular catabolic process0.031255519251148
GO:0009056catabolic process0.0364524795821157



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>

Cell Type
Ontology termp-valuen
animal cell8.07e-28679
eukaryotic cell8.07e-28679
native cell3.02e-22722
somatic cell1.31e-18588
mesodermal cell4.31e-13121
embryonic cell5.14e-13250
contractile cell5.29e-1059
somatic stem cell4.70e-09433
multi fate stem cell7.28e-09427
fibroblast1.40e-0876
muscle cell1.52e-0855
muscle precursor cell1.77e-0858
myoblast1.77e-0858
multi-potent skeletal muscle stem cell1.77e-0858
stem cell3.94e-08441
electrically responsive cell5.48e-0861
electrically active cell5.48e-0861
epithelial cell1.83e-07253
smooth muscle cell6.24e-0743
smooth muscle myoblast6.24e-0743
Uber Anatomy
Ontology termp-valuen
epithelial vesicle3.03e-1078
epithelial tube6.43e-10117
mesoderm3.28e-09315
mesoderm-derived structure3.28e-09315
presumptive mesoderm3.28e-09315
unilaminar epithelium7.54e-09148
artery8.12e-0942
arterial blood vessel8.12e-0942
arterial system8.12e-0942
cardiovascular system1.36e-08109
dense mesenchyme tissue1.70e-0873
somite3.00e-0871
presomitic mesoderm3.00e-0871
presumptive segmental plate3.00e-0871
dermomyotome3.00e-0871
trunk paraxial mesoderm3.00e-0871
vasculature3.06e-0878
vascular system3.06e-0878
trunk mesenchyme3.36e-08122
paraxial mesoderm4.16e-0872
presumptive paraxial mesoderm4.16e-0872
mesenchyme4.35e-08160
entire embryonic mesenchyme4.35e-08160
splanchnic layer of lateral plate mesoderm7.02e-0883
circulatory system7.20e-08112
trunk2.49e-07199
organism subdivision6.08e-07264
multilaminar epithelium7.43e-0783
systemic artery7.58e-0733
systemic arterial system7.58e-0733
epithelial tube open at both ends7.91e-0759
blood vessel7.91e-0759
blood vasculature7.91e-0759
vascular cord7.91e-0759


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)
MA0003.10.178364
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
MA0055.10.557638
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
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.12.25834
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.12.36034
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.12.30945
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
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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