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

Latest revision as of 11:19, 17 September 2013


Full id: C306_CD4_CD8_Neutrophils_Natural_CD19_CD14_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:112662692..112662695,+p@chr10:112662692..112662695
+
Hg19::chr10:120969026..120969030,+p@chr10:120969026..120969030
+
Hg19::chr10:70101463..70101469,+p14@HNRNPH3
Hg19::chr11:64540106..64540118,-p@chr11:64540106..64540118
-
Hg19::chr11:66412411..66412415,+p@chr11:66412411..66412415
+
Hg19::chr12:496389..496393,-p@chr12:496389..496393
-
Hg19::chr12:92506284..92506289,-p@chr12:92506284..92506289
-
Hg19::chr12:92517978..92517981,-p@chr12:92517978..92517981
-
Hg19::chr12:92521923..92521946,-p@chr12:92521923..92521946
-
Hg19::chr12:92525764..92525779,-p@chr12:92525764..92525779
-
Hg19::chr12:92529815..92529831,-p@chr12:92529815..92529831
-
Hg19::chr16:2805857..2805868,+p3@AB384460
Hg19::chr16:31196235..31196241,+p@chr16:31196235..31196241
+
Hg19::chr17:38720548..38720562,-p@chr17:38720548..38720562
-
Hg19::chr17:8397217..8397222,+p@chr17:8397217..8397222
+
Hg19::chr18:2734660..2734665,+p@chr18:2734660..2734665
+
Hg19::chr18:9218683..9218688,+p@chr18:9218683..9218688
+
Hg19::chr1:14076901..14076905,+p@chr1:14076901..14076905
+
Hg19::chr1:14084295..14084298,+p@chr1:14084295..14084298
+
Hg19::chr1:171519143..171519147,+p@chr1:171519143..171519147
+
Hg19::chr20:34304613..34304617,-p@chr20:34304613..34304617
-
Hg19::chr20:42837055..42837068,-p@chr20:42837055..42837068
-
Hg19::chr21:34931287..34931294,+p@chr21:34931287..34931294
+
Hg19::chr2:238604341..238604365,+p@chr2:238604341..238604365
+
Hg19::chr2:30378335..30378347,+p@chr2:30378335..30378347
+
Hg19::chr2:47171535..47171539,+p@chr2:47171535..47171539
+
Hg19::chr2:96959867..96959871,-p@chr2:96959867..96959871
-
Hg19::chr3:119181738..119181740,-p@chr3:119181738..119181740
-
Hg19::chr3:150332211..150332217,+p@chr3:150332211..150332217
+
Hg19::chr3:156869602..156869621,-p@chr3:156869602..156869621
-
Hg19::chr3:9932605..9932620,-p@chr3:9932605..9932620
-
Hg19::chr4:103713093..103713096,-p@chr4:103713093..103713096
-
Hg19::chr5:130638530..130638534,+p@chr5:130638530..130638534
+
Hg19::chr5:32592687..32592708,+p@chr5:32592687..32592708
+
Hg19::chr6:139489578..139489582,+p@chr6:139489578..139489582
+
Hg19::chr7:26234405..26234412,-p@chr7:26234405..26234412
-
Hg19::chr8:101725008..101725030,-p16@PABPC1
Hg19::chr8:101728081..101728097,-p22@PABPC1
Hg19::chr8:101959111..101959114,-p@chr8:101959111..101959114
-


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:0043489RNA stabilization0.00193016097290205
GO:0048255mRNA stabilization0.00193016097290205
GO:0008494translation activator activity0.00193016097290205
GO:0008143poly(A) binding0.00193016097290205
GO:0043487regulation of RNA stability0.00193016097290205
GO:0043488regulation of mRNA stability0.00193016097290205
GO:0006378mRNA polyadenylation0.00193016097290205
GO:0043631RNA polyadenylation0.00233525648573335
GO:0031124mRNA 3'-end processing0.00233525648573335
GO:0031123RNA 3'-end processing0.00250206052042859
GO:0051252regulation of RNA metabolic process0.00250206052042859
GO:0003727single-stranded RNA binding0.00250206052042859
GO:0003729mRNA binding0.00392631035513409
GO:0005681spliceosome0.0149051319574103
GO:0008135translation factor activity, nucleic acid binding0.0201165665842458
GO:0008380RNA splicing0.0211111356411162
GO:0006397mRNA processing0.0241080890144825
GO:0016071mRNA metabolic process0.0285234899328859
GO:0006396RNA processing0.0414815296807897



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
leukocyte2.23e-38136
nongranular leukocyte5.91e-35115
hematopoietic stem cell3.37e-33168
angioblastic mesenchymal cell3.37e-33168
hematopoietic cell3.56e-32177
hematopoietic lineage restricted progenitor cell4.51e-31120
hematopoietic oligopotent progenitor cell7.37e-31161
hematopoietic multipotent progenitor cell7.37e-31161
classical monocyte2.77e-2642
CD14-positive, CD16-negative classical monocyte2.77e-2642
defensive cell8.50e-2248
phagocyte8.50e-2248
myeloid leukocyte2.84e-2072
lymphocyte2.19e-1653
common lymphoid progenitor2.19e-1653
monopoietic cell5.34e-1659
monocyte5.34e-1659
monoblast5.34e-1659
promonocyte5.34e-1659
lymphoid lineage restricted progenitor cell6.10e-1652
macrophage dendritic cell progenitor8.91e-1661
granulocyte monocyte progenitor cell1.39e-1567
myeloid lineage restricted progenitor cell2.84e-1566
nucleate cell3.19e-1555
myeloid cell9.58e-15108
common myeloid progenitor9.58e-15108
intermediate monocyte1.95e-089
CD14-positive, CD16-positive monocyte1.95e-089
T cell1.99e-0825
pro-T cell1.99e-0825
mature alpha-beta T cell2.34e-0718
alpha-beta T cell2.34e-0718
immature T cell2.34e-0718
mature T cell2.34e-0718
immature alpha-beta T cell2.34e-0718
CD4-positive, alpha-beta T cell9.44e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.05e-1698
blood island2.05e-1698
hemolymphoid system1.95e-13108
bone marrow1.90e-1276
bone element2.68e-1182
immune system4.70e-1193
skeletal element6.45e-0990
skeletal system1.95e-07100
Disease
Ontology termp-valuen
cell type cancer1.54e-09143
cancer1.37e-08235
disease of cellular proliferation1.97e-08239
carcinoma2.25e-07106


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)
MA0003.12.29562e-09
MA0004.10.0566508
MA0006.10.014912
MA0007.10.0501273
MA0009.10.332084
MA0014.16.8361e-07
MA0017.10.096641
MA0019.10.777862
MA0024.10.254518
MA0025.10.439186
MA0027.11.8466
MA0028.10.0801195
MA0029.10.739626
MA0030.10.720769
MA0031.11.15909
MA0038.10.32871
MA0040.12.93909
MA0041.13.63364
MA0042.11.15076
MA0043.10.332327
MA0046.10.865123
MA0048.10.00142833
MA0050.11.15437
MA0051.11.10349
MA0052.10.755709
MA0055.10.00871109
MA0056.10
MA0057.10.00119221
MA0058.10.116428
MA0059.10.0276133
MA0060.10.0171632
MA0061.10.182822
MA0063.10
MA0066.10.100184
MA0067.10.597968
MA0068.10.486581
MA0069.10.320777
MA0070.10.312273
MA0071.10.588101
MA0072.10.308875
MA0073.12.57422e-11
MA0074.10.322317
MA0076.10.129848
MA0077.10.303076
MA0078.10.45889
MA0081.10.278085
MA0083.10.337888
MA0084.10.768496
MA0087.10.307032
MA0088.10.0876906
MA0089.10
MA0090.10.035827
MA0091.10.20991
MA0092.10.386895
MA0093.10.0154139
MA0095.10
MA0098.10
MA0100.10.346777
MA0101.10.617442
MA0103.10.169168
MA0105.10.0317322
MA0106.10.12076
MA0107.10.380955
MA0108.20.612085
MA0109.10
MA0111.10.356588
MA0113.10.129524
MA0114.10.0951836
MA0115.10.530757
MA0116.10.00669574
MA0117.10.36143
MA0119.10.0239211
MA0122.10.382044
MA0124.10.494979
MA0125.10.42437
MA0130.10
MA0131.10.161082
MA0132.10
MA0133.10
MA0135.10.936345
MA0136.10.337854
MA0139.10.00123664
MA0140.10.0810116
MA0141.10.113951
MA0142.10.194761
MA0143.10.129619
MA0144.10.00473992
MA0145.10.000241551
MA0146.10.000399001
MA0147.10.0373801
MA0148.10.505562
MA0149.10.0768601
MA0062.20.00144723
MA0035.20.0807052
MA0039.27.50587e-09
MA0138.20.151138
MA0002.20.217408
MA0137.20.0188925
MA0104.20.0169579
MA0047.20.367013
MA0112.20.00389731
MA0065.20.0151669
MA0150.10.585392
MA0151.10
MA0152.11.00374
MA0153.11.05663
MA0154.10.00348091
MA0155.10.000136934
MA0156.10.0861658
MA0157.11.00872
MA0158.10
MA0159.10.0376607
MA0160.10.251963
MA0161.10
MA0162.17.8067e-07
MA0163.10.00107154
MA0164.10.837054
MA0080.20.186056
MA0018.20.121488
MA0099.20.285408
MA0079.20
MA0102.20.803155
MA0258.10.0728937
MA0259.10.0411886
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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