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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.682618475962261,0

Latest revision as of 11:32, 17 September 2013


Full id: C878_Preadipocyte_Adipocyte_Mast_CD14_CD8_CD4_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:114167586..114167599,+p16@NNMT
Hg19::chr15:39486361..39486371,-p5@ENST00000560743
Hg19::chr15:39486372..39486387,-p4@ENST00000560743
Hg19::chr15:39486389..39486413,-p1@ENST00000560743
Hg19::chr15:39486417..39486445,-p2@ENST00000560743
Hg19::chr15:39486488..39486494,-p6@ENST00000560743
Hg19::chr15:39486515..39486531,-p3@ENST00000560743
Hg19::chr1:100503682..100503729,+p2@HIAT1
Hg19::chr1:185614334..185614338,-p@chr1:185614334..185614338
-


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:0008112nicotinamide N-methyltransferase activity0.00223713646532438
GO:0015904tetracycline transport0.0031954858870987
GO:0015307drug:hydrogen antiporter activity0.0031954858870987
GO:0015520tetracycline:hydrogen antiporter activity0.0031954858870987
GO:0008493tetracycline transporter activity0.0031954858870987
GO:0046677response to antibiotic0.0031954858870987
GO:0042895antibiotic transporter activity0.0031954858870987
GO:0015893drug transport0.0047527954656943
GO:0015238drug transporter activity0.00546686554372937
GO:0015299solute:hydrogen antiporter activity0.0060379569704045
GO:0015298solute:cation antiporter activity0.00876999965365704
GO:0008170N-methyltransferase activity0.00876999965365704
GO:0015300solute:solute antiporter activity0.00876999965365704
GO:0042493response to drug0.0100579274189454
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0127068590613247
GO:0015297antiporter activity0.0127068590613247
GO:0008168methyltransferase activity0.0344104638445509
GO:0016741transferase activity, transferring one-carbon groups0.0344104638445509
GO:0015291secondary active transmembrane transporter activity0.0421638748723498



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
skin fibroblast7.25e-3123
fibroblast5.11e-2776
preadipocyte of the breast1.45e-153
omentum preadipocyte2.83e-153
adipocyte of omentum tissue2.97e-153
preadipocyte3.25e-1412
receptor cell3.95e-126
sensory epithelial cell3.95e-126
olfactory epithelial cell3.95e-126
fat cell3.03e-1115
adipocyte of breast5.28e-112
Uber Anatomy
Ontology termp-valuen
omentum9.42e-296
peritoneum9.42e-296
abdominal cavity9.42e-296
visceral peritoneum9.42e-296
skin of body9.69e-2241
integument5.20e-1946
integumental system5.20e-1946
cavity lining4.59e-1412
serous membrane4.59e-1412
breast2.94e-1210
chest4.11e-1111
surface structure3.10e-0899
Disease
Ontology termp-valuen
musculoskeletal system disease5.76e-155
myotonic disease5.76e-155
muscle tissue disease5.76e-155
myopathy5.76e-155
muscular disease5.76e-155
myotonic dystrophy5.76e-155


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)
MA0003.10.0149552
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.0324647
MA0017.11.47956
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.13.09749
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.11.86771
MA0055.10.0199484
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.11.94461
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.11.95538
MA0088.10.0408613
MA0089.10
MA0090.11.66392
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.11.79761
MA0106.11.366
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.11.29512
MA0139.10.129876
MA0140.13.07568
MA0141.10.322254
MA0142.11.62667
MA0143.12.39416
MA0144.10.552298
MA0145.10.046841
MA0146.10.0794051
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.21.19307
MA0039.20.0189957
MA0138.20.608783
MA0002.22.0863
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.674448
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.225151
MA0155.10.0402662
MA0156.12.19106
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.29.34847e-05
MA0102.21.41188
MA0258.11.01999
MA0259.10.218904
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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