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Coexpression cluster:C767: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.17831577987551

Latest revision as of 11:30, 17 September 2013


Full id: C767_CD4_CD8_Neutrophils_Natural_Mast_Peripheral_CD19



Phase1 CAGE Peaks

Hg19::chr1:222818207..222818217,+p@chr1:222818207..222818217
+
Hg19::chr2:43451227..43451246,-p@chr2:43451227..43451246
-
Hg19::chr2:43451258..43451294,-p@chr2:43451258..43451294
-
Hg19::chr2:43451313..43451332,-p@chr2:43451313..43451332
-
Hg19::chr2:43451334..43451359,-p@chr2:43451334..43451359
-
Hg19::chr2:43452242..43452252,-p@chr2:43452242..43452252
-
Hg19::chr2:43452406..43452478,-p@chr2:43452406..43452478
-
Hg19::chr2:43452484..43452522,-p@chr2:43452484..43452522
-
Hg19::chr2:43452553..43452582,-p@chr2:43452553..43452582
-
Hg19::chr2:43452611..43452630,-p@chr2:43452611..43452630
-
Hg19::chr2:43452821..43452851,+p@chr2:43452821..43452851
+


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

No GOStat results

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
hemolymphoid system5.13e-09108
hematopoietic system8.01e-0998
blood island8.01e-0998


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)
MA0003.11.0887
MA0004.10.92264
MA0006.11.14056
MA0007.13.32388
MA0009.10.79061
MA0014.10.559573
MA0017.10.24363
MA0019.11.21992
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.13.94932
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.117.5589
MA0056.10
MA0057.10.176435
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.13.04853
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.552437
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.730303
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.467716
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.61153
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.11.11087
MA0105.10.360248
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.637178
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.02761
MA0146.10.0381286
MA0147.10.488526
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.0468759
MA0138.20.534556
MA0002.20.358551
MA0137.20.229531
MA0104.20.760822
MA0047.20.47109
MA0112.20.487949
MA0065.20.0286783
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.13.5791
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.11.7806
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.22.90119
MA0102.21.32663
MA0258.10.135061
MA0259.10.973858
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
CCNT2#90563.456109951070530.003468924173267830.0176228704996556
E2F6#1876104.561050665179448.90415381681673e-073.83797325825226e-05
MAX#414963.51957573218570.003153526355289020.01655530004122
MYC#4609104.747528974190376.01592453762049e-072.76296017055649e-05
PBX3#509047.96891370427060.001103670221799480.0076721388641185
POLR2A#5430112.147453176558070.0002231983422387430.00248620004960239
SETDB1#9869621.99274155164219.62882390616244e-085.67828763374195e-06
SIN3A#25942115.408884726815148.61479924770236e-096.62533887062435e-07
SMARCB1#659846.637351193148150.002175555385092920.0125518080247332
SMC3#912645.470884670884670.004404703538339480.020869338694399
TAF7#687944.15747978360870.01167992922291530.0426428066878296
ZEB1#693546.141248006379590.002893399946065070.0156458422370865



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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