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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0502604313716981,

Latest revision as of 11:22, 17 September 2013


Full id: C416_CD4_Neutrophils_CD8_Natural_CD19_CD14_Peripheral



Phase1 CAGE Peaks

Hg19::chr12:432372..432377,-p3@KDM5A
Hg19::chr14:58759862..58759865,-p@chr14:58759862..58759865
-
Hg19::chr15:63867377..63867381,+p@chr15:63867377..63867381
+
Hg19::chr15:93440362..93440368,+p@chr15:93440362..93440368
+
Hg19::chr16:89942255..89942258,+p@chr16:89942255..89942258
+
Hg19::chr17:47907569..47907575,+p@chr17:47907569..47907575
+
Hg19::chr17:76693404..76693408,-p@chr17:76693404..76693408
-
Hg19::chr19:16720749..16720753,-p@chr19:16720749..16720753
-
Hg19::chr1:14085673..14085677,+p@chr1:14085673..14085677
+
Hg19::chr1:171455261..171455278,+p@chr1:171455261..171455278
+
Hg19::chr1:65394459..65394461,-p@chr1:65394459..65394461
-
Hg19::chr1:67405973..67405977,+p@chr1:67405973..67405977
+
Hg19::chr2:197017976..197017980,-p@chr2:197017976..197017980
-
Hg19::chr2:225422591..225422605,-p8@CUL3
Hg19::chr2:225434670..225434674,-p6@CUL3
Hg19::chr2:54194783..54194785,-p@chr2:54194783..54194785
-
Hg19::chr5:93340701..93340703,-p@chr5:93340701..93340703
-
Hg19::chr6:131948461..131948465,-p@chr6:131948461..131948465
-
Hg19::chr6:155101505..155101509,+p@chr6:155101505..155101509
+
Hg19::chr6:4022409..4022413,+p@chr6:4022409..4022413
+
Hg19::chr7:151950594..151950600,-p@chr7:151950594..151950600
-
Hg19::chr7:155448253..155448257,+p@chr7:155448253..155448257
+
Hg19::chr7:32912993..32912997,-p@chr7:32912993..32912997
-
Hg19::chr9:86593238..86593252,-p3@HNRNPK
Hg19::chrX:70754993..70754996,+p@chrX:70754993..70754996
+


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:0031461cullin-RING ubiquitin ligase complex0.0203991522430237
GO:0031625ubiquitin protein ligase binding0.0203991522430237
GO:0000082G1/S transition of mitotic cell cycle0.0203991522430237
GO:0008629induction of apoptosis by intracellular signals0.0203991522430237
GO:0000151ubiquitin ligase complex0.0286154774520193
GO:0051329interphase of mitotic cell cycle0.0286154774520193
GO:0051325interphase0.0286154774520193
GO:0007050cell cycle arrest0.0286154774520193
GO:0006917induction of apoptosis0.0334546096785588
GO:0012502induction of programmed cell death0.0334546096785588
GO:0045786negative regulation of progression through cell cycle0.0334546096785588
GO:0008284positive regulation of cell proliferation0.0334546096785588
GO:0043065positive regulation of apoptosis0.0334546096785588
GO:0043068positive regulation of programmed cell death0.0334546096785588
GO:0006511ubiquitin-dependent protein catabolic process0.0334546096785588
GO:0043632modification-dependent macromolecule catabolic process0.0334546096785588
GO:0019941modification-dependent protein catabolic process0.0334546096785588
GO:0051603proteolysis involved in cellular protein catabolic process0.0334546096785588
GO:0044257cellular protein catabolic process0.0334546096785588
GO:0019899enzyme binding0.0334546096785588
GO:0000278mitotic cell cycle0.0334546096785588
GO:0000074regulation of progression through cell cycle0.0334546096785588
GO:0030163protein catabolic process0.0334546096785588
GO:0051726regulation of cell cycle0.0334546096785588
GO:0022403cell cycle phase0.0334546096785588
GO:0043285biopolymer catabolic process0.0393712033003214
GO:0042127regulation of cell proliferation0.0393712033003214
GO:0044265cellular macromolecule catabolic process0.0421143788243069
GO:0006512ubiquitin cycle0.0421143788243069
GO:0042981regulation of apoptosis0.0421143788243069
GO:0043067regulation of programmed cell death0.0421143788243069
GO:0022402cell cycle process0.0429275089289218
GO:0009057macromolecule catabolic process0.0429275089289218
GO:0005794Golgi apparatus0.0463314078722269
GO:0008283cell proliferation0.0482456140350877



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
leukocyte2.82e-44136
hematopoietic stem cell4.41e-41168
angioblastic mesenchymal cell4.41e-41168
nongranular leukocyte1.99e-37115
hematopoietic cell2.92e-37177
hematopoietic lineage restricted progenitor cell3.02e-37120
hematopoietic oligopotent progenitor cell3.71e-37161
hematopoietic multipotent progenitor cell3.71e-37161
myeloid leukocyte2.14e-2172
classical monocyte8.00e-2042
CD14-positive, CD16-negative classical monocyte8.00e-2042
myeloid cell2.66e-19108
common myeloid progenitor2.66e-19108
macrophage dendritic cell progenitor6.51e-1961
myeloid lineage restricted progenitor cell1.17e-1866
granulocyte monocyte progenitor cell1.81e-1867
defensive cell2.31e-1848
phagocyte2.31e-1848
monopoietic cell5.66e-1859
monocyte5.66e-1859
monoblast5.66e-1859
promonocyte5.66e-1859
nucleate cell3.19e-1755
lymphocyte3.70e-1753
common lymphoid progenitor3.70e-1753
lymphoid lineage restricted progenitor cell4.55e-1752
mature alpha-beta T cell2.93e-0918
alpha-beta T cell2.93e-0918
immature T cell2.93e-0918
mature T cell2.93e-0918
immature alpha-beta T cell2.93e-0918
T cell4.97e-0925
pro-T cell4.97e-0925
lymphocyte of B lineage1.39e-0724
pro-B cell1.39e-0724
intermediate monocyte1.00e-069
CD14-positive, CD16-positive monocyte1.00e-069
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.18e-2198
blood island1.18e-2198
hemolymphoid system5.75e-20108
bone marrow1.45e-1476
immune system2.74e-1493
bone element6.33e-1482
skeletal element2.12e-0990
adult organism3.56e-08114
skeletal system5.86e-08100
blood1.29e-0715
haemolymphatic fluid1.29e-0715
organism substance1.29e-0715


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)
MA0003.12.55068e-09
MA0004.10.130779
MA0006.10.0525289
MA0007.10.120068
MA0009.10.480543
MA0014.12.83616e-06
MA0017.10.0687354
MA0019.10.644268
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.10.0589063
MA0029.10.407394
MA0030.11.02886
MA0031.10.344829
MA0038.10.569682
MA0040.11.06051
MA0041.11.38763
MA0042.10.389397
MA0043.11.20842
MA0046.10.47108
MA0048.10.0169194
MA0050.10.781212
MA0051.10.192868
MA0052.11.87776
MA0055.10.000754127
MA0056.10
MA0057.10.015143
MA0058.10.0802423
MA0059.10.0796335
MA0060.10.017391
MA0061.10.0591371
MA0063.10
MA0066.10.196017
MA0067.10.769322
MA0068.10.0364071
MA0069.10.467738
MA0070.10.458064
MA0071.10.170069
MA0072.10.454189
MA0073.13.93678e-11
MA0074.10.19236
MA0076.10.0879186
MA0077.10.44756
MA0078.10.263604
MA0081.10.07971
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.10.00415386
MA0089.10
MA0090.10.0951695
MA0091.11.32898
MA0092.10.724515
MA0093.10.053707
MA0095.10
MA0098.10
MA0100.10.205224
MA0101.10.202181
MA0103.10.184112
MA0105.10.0974258
MA0106.10.224407
MA0107.10.293146
MA0108.20.342362
MA0109.10
MA0111.10.334615
MA0113.10.236174
MA0114.10.0284198
MA0115.10.697973
MA0116.10.126338
MA0117.10.513502
MA0119.10.25231
MA0122.10.53644
MA0124.10.659634
MA0125.10.583056
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.12.18453
MA0136.10.200538
MA0139.10.0102505
MA0140.10.168354
MA0141.10.0788154
MA0142.10.85557
MA0143.10.665621
MA0144.10.104952
MA0145.10.000771166
MA0146.10.000594916
MA0147.10.031895
MA0148.10.876759
MA0149.10.162171
MA0062.20.0113502
MA0035.20.50217
MA0039.23.44083e-05
MA0138.20.264522
MA0002.20.0700986
MA0137.20.0615777
MA0104.20.0172311
MA0047.20.617535
MA0112.20.00476632
MA0065.20.0230378
MA0150.10.307678
MA0151.10
MA0152.10.513688
MA0153.10.567879
MA0154.10.0110055
MA0155.10.00401501
MA0156.10.224407
MA0157.10.298026
MA0158.10
MA0159.10.0320844
MA0160.10.154993
MA0161.10
MA0162.11.4624e-05
MA0163.10.00125667
MA0164.10.68636
MA0080.20.0537406
MA0018.20.225392
MA0099.20.172833
MA0079.24.82164e-16
MA0102.20.983247
MA0258.10.239173
MA0259.10.0344451
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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