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

Latest revision as of 11:10, 17 September 2013


Full id: C269_Basophils_Mast_Eosinophils_mature_CD14_chorionic_CD4



Phase1 CAGE Peaks

Hg19::chr14:75745523..75745537,+p1@FOS
Hg19::chr14:75745802..75745826,-p@chr14:75745802..75745826
-
Hg19::chr14:75746579..75746605,+p9@FOS
Hg19::chr14:75746613..75746623,+p11@FOS
Hg19::chr14:75746687..75746702,+p10@FOS
Hg19::chr14:75746705..75746720,+p8@FOS
Hg19::chr14:75746722..75746777,+p2@FOS
Hg19::chr14:75746781..75746799,+p6@FOS
Hg19::chr14:75747250..75747267,+p5@FOS
Hg19::chr14:75747296..75747329,+p4@FOS
Hg19::chr14:75747492..75747516,+p@chr14:75747492..75747516
+
Hg19::chr14:75747550..75747561,+p@chr14:75747550..75747561
+
Hg19::chr14:75747573..75747583,+p@chr14:75747573..75747583
+
Hg19::chr14:75747611..75747620,+p@chr14:75747611..75747620
+
Hg19::chr14:75747625..75747645,+p@chr14:75747625..75747645
+
Hg19::chr14:75747656..75747717,+p@chr14:75747656..75747717
+
Hg19::chr14:75747782..75747798,+p@chr14:75747782..75747798
+
Hg19::chr14:75747827..75747836,+p@chr14:75747827..75747836
+
Hg19::chr14:75747960..75747972,+p@chr14:75747960..75747972
+
Hg19::chr14:75748018..75748039,+p@chr14:75748018..75748039
+
Hg19::chr14:75748187..75748202,+p@chr14:75748187..75748202
+
Hg19::chr14:75748263..75748319,+p@chr14:75748263..75748319
+
Hg19::chr14:75748371..75748442,+p1@S65140
Hg19::chr14:75748616..75748661,+p2@S65140
Hg19::chr19:45972203..45972226,+p5@FOSB
Hg19::chr19:45973899..45973920,+p@chr19:45973899..45973920
+
Hg19::chr19:45973962..45973979,+p@chr19:45973962..45973979
+
Hg19::chr19:45974005..45974026,+p11@FOSB
Hg19::chr19:45974032..45974054,+p9@FOSB
Hg19::chr19:45974146..45974170,+p7@FOSB
Hg19::chr19:45974438..45974449,+p26@FOSB
Hg19::chr19:45975749..45975760,+p@chr19:45975749..45975760
+
Hg19::chr19:45975995..45976038,+p2@AF432216
Hg19::chr19:45976177..45976190,+p6@AF432216
Hg19::chr19:45976666..45976678,+p3@AF432216
Hg19::chr19:45977115..45977124,+p@chr19:45977115..45977124
+
Hg19::chr19:45977207..45977222,+p@chr19:45977207..45977222
+
Hg19::chr19:45977304..45977312,+p@chr19:45977304..45977312
+
Hg19::chr19:45977321..45977334,+p@chr19:45977321..45977334
+
Hg19::chr19:45977344..45977355,+p@chr19:45977344..45977355
+
Hg19::chr19:45977475..45977486,+p@chr19:45977475..45977486
+
Hg19::chr19:45977515..45977522,+p@chr19:45977515..45977522
+
Hg19::chr19:45977611..45977627,+p@chr19:45977611..45977627
+
Hg19::chr19:45977632..45977642,+p@chr19:45977632..45977642
+
Hg19::chr19:45977697..45977713,+p4@FOSB
Hg19::chr19:45977759..45977770,+p10@FOSB
Hg19::chr19:45977916..45977932,+p13@FOSB
Hg19::chr19:45977993..45978005,+p6@FOSB
Hg19::chr19:45978061..45978070,+p24@FOSB


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

p.valueFDRnGenesnPathwayName
1.99497924496294e-050.006181011697713452128Osteoclast differentiation (KEGG):04380
2.92938943019595e-050.006181011697713452155TGF-beta Receptor Signaling Pathway (Wikipathways):WP366
8.97102502502407e-060.00567865884084024286{JUN,88} (Static Module):NA



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:0046983protein dimerization activity0.00711510319422719
GO:0006357regulation of transcription from RNA polymerase II promoter0.00711510319422719
GO:0006366transcription from RNA polymerase II promoter0.0108672074601084
GO:0043565sequence-specific DNA binding0.0151367636305051
GO:0006306DNA methylation0.0207554734031237
GO:0006305DNA alkylation0.0207554734031237
GO:0006304DNA modification0.0210525571751405
GO:0003700transcription factor activity0.0210525571751405
GO:0004289subtilase activity0.0210525571751405
GO:0003704specific RNA polymerase II transcription factor activity0.0211114637320105
GO:0043414biopolymer methylation0.0221429353030901
GO:0040029regulation of gene expression, epigenetic0.0293102504025579
GO:0032259methylation0.0299662068333565
GO:0007275multicellular organismal development0.0300828750979383
GO:0046982protein heterodimerization activity0.0365019430155593
GO:0003690double-stranded DNA binding0.0365019430155593
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0377712194593578
GO:0006730one-carbon compound metabolic process0.0377712194593578
GO:0043566structure-specific DNA binding0.0377712194593578
GO:0032502developmental process0.0377712194593578
GO:0006355regulation of transcription, DNA-dependent0.0377712194593578
GO:0006351transcription, DNA-dependent0.0377712194593578
GO:0032774RNA biosynthetic process0.0377712194593578
GO:0003677DNA binding0.0377712194593578
GO:0045449regulation of transcription0.0377712194593578
GO:0045892negative regulation of transcription, DNA-dependent0.0377712194593578
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0377712194593578
GO:0005667transcription factor complex0.0377712194593578
GO:0006350transcription0.0377712194593578
GO:0032501multicellular organismal process0.0377712194593578
GO:0010468regulation of gene expression0.0377712194593578
GO:0031323regulation of cellular metabolic process0.0385252847918647
GO:0019222regulation of metabolic process0.0404684885098427
GO:0016070RNA metabolic process0.0404684885098427
GO:0003702RNA polymerase II transcription factor activity0.0417237654697631
GO:0006954inflammatory response0.0417237654697631
GO:0016481negative regulation of transcription0.0417237654697631
GO:0007610behavior0.0417237654697631
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0440945903855701
GO:0004252serine-type endopeptidase activity0.0448697405908615
GO:0008236serine-type peptidase activity0.0477218639162913
GO:0017171serine hydrolase activity0.0477218639162913
GO:0031324negative regulation of cellular metabolic process0.0477218639162913



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
classical monocyte7.85e-4142
CD14-positive, CD16-negative classical monocyte7.85e-4142
myeloid leukocyte3.21e-3472
defensive cell8.09e-3448
phagocyte8.09e-3448
leukocyte6.28e-30136
granulocyte monocyte progenitor cell6.32e-2967
macrophage dendritic cell progenitor1.44e-2761
myeloid lineage restricted progenitor cell3.09e-2666
monopoietic cell1.66e-2559
monocyte1.66e-2559
monoblast1.66e-2559
promonocyte1.66e-2559
hematopoietic lineage restricted progenitor cell6.25e-24120
nongranular leukocyte6.09e-23115
hematopoietic stem cell8.88e-20168
angioblastic mesenchymal cell8.88e-20168
myeloid cell3.31e-19108
common myeloid progenitor3.31e-19108
hematopoietic oligopotent progenitor cell6.59e-19161
hematopoietic multipotent progenitor cell6.59e-19161
hematopoietic cell1.21e-17177
stuff accumulating cell1.08e-1687
intermediate monocyte1.81e-109
CD14-positive, CD16-positive monocyte1.81e-109
connective tissue cell8.86e-09361
granulocyte1.92e-088
mesenchymal cell2.92e-08354
CD4-positive, alpha-beta T cell9.09e-086
Uber Anatomy
Ontology termp-valuen
bone marrow5.43e-2576
bone element2.11e-2382
skeletal element4.97e-2390
skeletal system4.19e-20100
hematopoietic system5.14e-2098
blood island5.14e-2098
immune system1.39e-1893
hemolymphoid system1.20e-16108
connective tissue5.44e-09371


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)
MA0003.11.98642e-06
MA0004.11.73323
MA0006.10.375359
MA0007.10.516216
MA0009.10.729191
MA0014.10.594753
MA0017.10.0101672
MA0019.10.0819566
MA0024.10.193834
MA0025.10.3631
MA0027.11.74826
MA0028.10.0076558
MA0029.10.206098
MA0030.10.198787
MA0031.10.15963
MA0038.11.28813
MA0040.10.209871
MA0041.10.0369855
MA0042.10.0289066
MA0043.10.263979
MA0046.10.256123
MA0048.10.694438
MA0050.10.0291141
MA0051.10.0624698
MA0052.10.21238
MA0055.10.727155
MA0056.10
MA0057.10.0549005
MA0058.12.48979
MA0059.15.36772
MA0060.10.215973
MA0061.10.0364588
MA0063.10
MA0066.15.89844
MA0067.10.514146
MA0068.15.29034
MA0069.10.253439
MA0070.10.245703
MA0071.10.420623
MA0072.10.24262
MA0073.12.33949
MA0074.10.485229
MA0076.10.0733944
MA0077.10.237364
MA0078.10.104384
MA0081.10.168037
MA0083.10.269067
MA0084.10.679402
MA0087.10.240948
MA0088.10.0430139
MA0089.10
MA0090.10.209563
MA0091.10.0328063
MA0092.11.5283
MA0093.13.35006
MA0095.10
MA0098.10
MA0100.10.243929
MA0101.10.392648
MA0103.10.195176
MA0105.10.125452
MA0106.10.0803211
MA0107.10.357521
MA0108.20.157861
MA0109.10
MA0111.10.0915545
MA0113.10.294463
MA0114.10.103664
MA0115.10.449785
MA0116.10.0481717
MA0117.10.290704
MA0119.10.511038
MA0122.10.309767
MA0124.10.415762
MA0125.10.921904
MA0130.10
MA0131.10.363777
MA0132.10
MA0133.10
MA0135.10.285448
MA0136.10.0666752
MA0139.10.680956
MA0140.10.415677
MA0141.11.17489
MA0142.10.436942
MA0143.10.0874172
MA0144.13.5442
MA0145.10.901664
MA0146.10.129978
MA0147.11.4063
MA0148.10.0387369
MA0149.10.0465992
MA0062.20.0330991
MA0035.20.185398
MA0039.20.000417237
MA0138.20.342023
MA0002.22.45377
MA0137.22.57439
MA0104.21.52877
MA0047.20.261058
MA0112.20.514308
MA0065.20.108507
MA0150.10.0787122
MA0151.10
MA0152.10.0518114
MA0153.10.336269
MA0154.11.27586
MA0155.10.746911
MA0156.10.256234
MA0157.10.126996
MA0158.10
MA0159.10.00245494
MA0160.10.0431262
MA0161.10
MA0162.10.015859
MA0163.10.218219
MA0164.10.0928538
MA0080.20.101379
MA0018.20.276679
MA0099.20.0519295
MA0079.25.13561e-05
MA0102.20.713248
MA0258.12.51769
MA0259.10.859914
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
KAT2A#26488100.586122448981.86712808033721e-143.16560048023276e-12
POLR2A#5430492.147453176558075.40215358511943e-171.10410081854459e-14
TAF1#6872231.56918499126820.008854419286335490.0336075990640206
TAF7#6879214.899886887824532.03765091642971e-102.10494781464889e-08
ZBTB7A#51341152.250584482002830.001624432017818540.0101674490895931



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

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