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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:35, 17 September 2013


Full id: C996_CD4_CD8_Natural_CD19_Whole_blood_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:64512524..64512536,-p11@RASGRP2
Hg19::chr11:64512542..64512604,-p4@RASGRP2
Hg19::chr13:74707811..74707813,-p@chr13:74707811..74707813
-
Hg19::chr14:91884115..91884127,-p4@CCDC88C
Hg19::chr1:101707580..101707583,+p@chr1:101707580..101707583
+
Hg19::chr4:40232957..40232960,+p@chr4:40232957..40232960
+
Hg19::chr7:2981171..2981174,-p@chr7:2981171..2981174
-
Hg19::chr7:2983379..2983381,-p@chr7:2983379..2983381
-


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:0031648protein destabilization0.00682905290600423
GO:0043621protein self-association0.0143370005756672
GO:0030165PDZ domain binding0.0143370005756672
GO:0005626insoluble fraction0.0143370005756672
GO:0031647regulation of protein stability0.0143370005756672
GO:0051260protein homooligomerization0.0174407218005431
GO:0001932regulation of protein amino acid phosphorylation0.0174407218005431
GO:0033238regulation of amine metabolic process0.0174407218005431
GO:0006521regulation of amino acid metabolic process0.0174407218005431
GO:0051259protein oligomerization0.0181053835448897
GO:0042325regulation of phosphorylation0.0181053835448897
GO:0051174regulation of phosphorus metabolic process0.0181053835448897
GO:0019220regulation of phosphate metabolic process0.0181053835448897
GO:0019904protein domain specific binding0.0309176447148182
GO:0016055Wnt receptor signaling pathway0.0329376168016293



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
lymphocyte4.90e-4253
common lymphoid progenitor4.90e-4253
lymphoid lineage restricted progenitor cell3.97e-4152
nucleate cell8.82e-4055
nongranular leukocyte3.41e-31115
leukocyte3.49e-30136
hematopoietic lineage restricted progenitor cell1.78e-27120
hematopoietic stem cell5.92e-27168
angioblastic mesenchymal cell5.92e-27168
hematopoietic cell1.11e-26177
hematopoietic oligopotent progenitor cell3.81e-24161
hematopoietic multipotent progenitor cell3.81e-24161
mature alpha-beta T cell2.45e-2018
alpha-beta T cell2.45e-2018
immature T cell2.45e-2018
mature T cell2.45e-2018
immature alpha-beta T cell2.45e-2018
T cell2.15e-1925
pro-T cell2.15e-1925
lymphocyte of B lineage4.55e-1924
pro-B cell4.55e-1924
B cell1.22e-1414
CD8-positive, alpha-beta T cell6.71e-1311
CD4-positive, alpha-beta T cell2.71e-086
circulating cell7.91e-076
Uber Anatomy
Ontology termp-valuen
adult organism3.90e-17114
blood2.80e-1615
haemolymphatic fluid2.80e-1615
organism substance2.80e-1615
hematopoietic system1.58e-1098
blood island1.58e-1098
hemolymphoid system1.06e-09108
hemopoietic organ2.55e-077
immune organ2.55e-077


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)
MA0003.12.40022
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.12.6969
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
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.632427
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
MA0073.10.0719479
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.441522
MA0089.10
MA0090.10.391903
MA0091.11.16006
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.988431
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.220937
MA0146.10.418694
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.21.46411
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.458158
MA0065.21.27835
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.43752
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.378102
MA0163.10.75401
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.23.09265
MA0102.21.46209
MA0258.10.209744
MA0259.10.699589
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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