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{{Coexpression_clusters
{
|full_id=C1039_CD4_NK_CD8_CD19_Natural_Whole_chronic
 

Latest revision as of 11:36, 17 September 2013


Full id: C1039_CD4_NK_CD8_CD19_Natural_Whole_chronic



Phase1 CAGE Peaks

Hg19::chr14:91696341..91696361,+p@chr14:91696341..91696361
+
Hg19::chr19:39225003..39225020,-p@chr19:39225003..39225020
-
Hg19::chr2:191929516..191929561,+p@chr2:191929516..191929561
+
Hg19::chr2:231792452..231792463,-p@chr2:231792452..231792463
-
Hg19::chr4:110980983..110980988,-p17@ELOVL6
Hg19::chr5:66456034..66456066,+p@chr5:66456034..66456066
+
Hg19::chr5:80037077..80037109,+p@chr5:80037077..80037109
+
Hg19::chr9:92316442..92316457,+p2@ENST00000444374


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:0030497fatty acid elongation0.00129518426939833
GO:0030176integral to endoplasmic reticulum membrane0.0179167157266769
GO:0031227intrinsic to endoplasmic reticulum membrane0.0179167157266769
GO:0006633fatty acid biosynthetic process0.0179167157266769
GO:0046394carboxylic acid biosynthetic process0.0179167157266769
GO:0016053organic acid biosynthetic process0.0179167157266769
GO:0031301integral to organelle membrane0.0246085011185682
GO:0031300intrinsic to organelle membrane0.0246085011185682
GO:0006631fatty acid metabolic process0.0274866883838978
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.0319478786451587
GO:0032787monocarboxylic acid metabolic process0.0319478786451587
GO:0016746transferase activity, transferring acyl groups0.0319478786451587
GO:0008610lipid biosynthetic process0.0331766432084341
GO:0005789endoplasmic reticulum membrane0.0403234035872679
GO:0042175nuclear envelope-endoplasmic reticulum network0.0403234035872679
GO:0044432endoplasmic reticulum part0.0420934887554456



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
mature alpha-beta T cell5.23e-4618
alpha-beta T cell5.23e-4618
immature T cell5.23e-4618
mature T cell5.23e-4618
immature alpha-beta T cell5.23e-4618
T cell1.15e-3725
pro-T cell1.15e-3725
CD8-positive, alpha-beta T cell3.40e-2911
lymphoid lineage restricted progenitor cell4.65e-2252
lymphocyte1.41e-2153
common lymphoid progenitor1.41e-2153
nucleate cell1.16e-2055
CD4-positive, alpha-beta T cell7.67e-146
thymocyte1.28e-112
double negative thymocyte1.28e-112
double-positive, alpha-beta thymocyte1.28e-112
DN4 thymocyte1.28e-112
DN1 thymic pro-T cell1.28e-112
DN2 thymocyte1.28e-112
DN3 thymocyte1.28e-112
immature single positive thymocyte1.28e-112
early T lineage precursor1.28e-112
nongranular leukocyte1.72e-10115
leukocyte1.93e-09136
natural killer cell4.70e-083
pro-NK cell4.70e-083
naive T cell6.89e-083
single nucleate cell8.77e-083
mononuclear cell8.77e-083
hematopoietic lineage restricted progenitor cell1.57e-07120
hematopoietic stem cell6.68e-07168
angioblastic mesenchymal cell6.68e-07168
innate effector T cell8.21e-071
immature NK T cell8.21e-071
effector T cell8.21e-071
mature NK T cell8.21e-071
immature NK T cell stage IV8.21e-071
immature NK T cell stage I8.21e-071
immature NK T cell stage II8.21e-071
immature NK T cell stage III8.21e-071


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)
MA0003.10.00101002
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.11.12793
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.326687
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.11.01596
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.11.04489
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.12.5277
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.12.37243
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.11.72156
MA0143.11.49284
MA0144.10.218541
MA0145.10.220937
MA0146.10.00761723
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.942487
MA0035.20.515566
MA0039.20.00915579
MA0138.20.653421
MA0002.21.01797
MA0137.20.86081
MA0104.20.189646
MA0047.20.586412
MA0112.20.79629
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.974997
MA0155.10.43752
MA0156.11.55957
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.141536
MA0164.10.627336
MA0080.21.48508
MA0018.20.599912
MA0099.20.523145
MA0079.20.0171409
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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
SPI1#668844.102161754261360.01027800662400760.0381906547765586



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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