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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:46, 17 September 2013


Full id: C1500_Melanocyte_Monocytederived_CD14_melanoma_retina_Macrophage_Mast



Phase1 CAGE Peaks

Hg19::chr2:170335297..170335305,+p2@BBS5
Hg19::chr3:126675836..126675847,+p5@CHCHD6
Hg19::chr3:126675939..126675962,+p3@CHCHD6
Hg19::chr3:126675964..126675975,+p6@CHCHD6
Hg19::chr3:126675978..126675988,+p4@CHCHD6
Hg19::chr3:126676020..126676029,+p9@CHCHD6


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:0005929cilium0.0120687625103026
GO:0007601visual perception0.021880764551199
GO:0050953sensory perception of light stimulus0.021880764551199
GO:0042995cell projection0.0230336747910043



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
melanocyte6.30e-4410
melanoblast6.30e-4410
macrophage2.16e-376
pigment cell3.24e-3114
adult endothelial progenitor cell1.07e-283
light melanocyte6.84e-283
neurecto-epithelial cell1.15e-2120
histamine secreting cell1.41e-165
biogenic amine secreting cell1.41e-165
granulocytopoietic cell1.41e-165
mast cell1.41e-165
mast cell progenitor1.41e-165
basophil mast progenitor cell1.41e-165
columnar/cuboidal epithelial cell7.14e-1627
myeloid lineage restricted progenitor cell1.25e-1466
granulocyte monocyte progenitor cell2.17e-1467
myeloid leukocyte2.75e-1372
stuff accumulating cell4.42e-1387
ecto-epithelial cell1.85e-1234
dark melanocyte1.73e-101
migratory neural crest cell1.07e-0941
endocrine cell1.84e-099
monopoietic cell9.37e-0959
monocyte9.37e-0959
monoblast9.37e-0959
promonocyte9.37e-0959
macrophage dendritic cell progenitor1.94e-0861
myeloid cell2.51e-08108
common myeloid progenitor2.51e-08108
hematopoietic lineage restricted progenitor cell2.49e-07120
Uber Anatomy
Ontology termp-valuen
bone marrow1.66e-1276
bone element1.77e-1182
skeletal element2.56e-1090
immune system6.22e-1093
hematopoietic system2.41e-0998
blood island2.41e-0998
skeletal system4.00e-09100
hemolymphoid system2.51e-08108
Disease
Ontology termp-valuen
melanoma1.97e-192


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.11.69574
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.11.34656
MA0051.12.6843
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.93637
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.17.13504
MA0103.10.381434
MA0105.11.34409
MA0106.10.70837
MA0107.16.34858
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.13.97537
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.232472
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.200862
MA0138.20.765223
MA0002.24.64448
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.21.65732
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.00575781
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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
NFKB1#479054.57338618682820.00102196259371130.00724741979524778



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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