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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 12:33, 17 September 2013


Full id: C3833_Dendritic_lymph_dura_CD14_duodenum_vein_left



Phase1 CAGE Peaks

Hg19::chr19:7805780..7805799,-p@chr19:7805780..7805799
-
Hg19::chr19:7807611..7807619,-p1@AK057212
Hg19::chr19:7812412..7812426,-p2@CD209


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:0046795intracellular virion transport0.0010891322265395
GO:0046794virion transport0.0010891322265395
GO:0046968peptide antigen transport0.0010891322265395
GO:0042607exogenous peptide antigen binding0.0010891322265395
GO:0019062virion attachment to host cell surface receptor0.0013069586718474
GO:0046790virion binding0.00140946523434524
GO:0007159leukocyte adhesion0.00140946523434524
GO:0044409entry into host0.00140946523434524
GO:0030260entry into host cell0.00140946523434524
GO:0046718entry of virus into host cell0.00140946523434524
GO:0007157heterophilic cell adhesion0.00140946523434524
GO:0052126movement in host environment0.00140946523434524
GO:0019048virus-host interaction0.00140946523434524
GO:0051828entry into other organism during symbiotic interaction0.00140946523434524
GO:0019059initiation of viral infection0.00140946523434524
GO:0051806entry into cell of other organism during symbiotic interaction0.00140946523434524
GO:0052192movement in environment of other organism during symbiotic interaction0.00140946523434524
GO:0005537mannose binding0.00145217630205267
GO:0009405pathogenesis0.00149039146789616
GO:0009988cell-cell recognition0.0015247851171553
GO:0048029monosaccharide binding0.00176335693820681
GO:0042605peptide antigen binding0.001782216370701
GO:0051701interaction with host0.00208355730294514
GO:0019079viral genome replication0.00263206954747047
GO:0044403symbiosis, encompassing mutualism through parasitism0.00268094086532801
GO:0044419interspecies interaction between organisms0.00268094086532801
GO:0008037cell recognition0.0030340112025029
GO:0015833peptide transport0.0030340112025029
GO:0019058viral infectious cycle0.0037556283673776
GO:0022415viral reproductive process0.00413870246085011
GO:0048002antigen processing and presentation of peptide antigen0.00737799250236437
GO:0003823antigen binding0.0120485252560932
GO:0010324membrane invagination0.012621120507546
GO:0006897endocytosis0.012621120507546
GO:0042277peptide binding0.0129451144640124
GO:0016044membrane organization and biogenesis0.0171840862409566
GO:0022414reproductive process0.0179559637348405
GO:0051704multi-organism process0.0188964441304604
GO:0016337cell-cell adhesion0.0188964441304604
GO:0005529sugar binding0.0188964441304604
GO:0019882antigen processing and presentation0.0220482865372631
GO:0030246carbohydrate binding0.0247907240136135
GO:0016192vesicle-mediated transport0.0306983315945553
GO:0046907intracellular transport0.0450504693704976
GO:0022610biological adhesion0.0454594320642575
GO:0007155cell adhesion0.0454594320642575



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
macrophage1.16e-196
monopoietic cell1.70e-0759
monocyte1.70e-0759
monoblast1.70e-0759
promonocyte1.70e-0759
macrophage dendritic cell progenitor3.73e-0761
Uber Anatomy
Ontology termp-valuen
adult organism9.32e-21114
cardiac chamber1.35e-103
cardiac atrium1.24e-072
future cardiac atrium1.24e-072
immune system1.49e-0793
Disease
Ontology termp-valuen
heart disease4.02e-072


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
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.11.74184
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
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
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
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
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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