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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:17, 17 September 2013


Full id: C299_CD14CD16_Eosinophils_Neutrophils_CD14_Whole_Basophils_blood



Phase1 CAGE Peaks

Hg19::chr11:67051096..67051110,+p@chr11:67051096..67051110
+
Hg19::chr11:67051146..67051171,+p@chr11:67051146..67051171
+
Hg19::chr11:67056068..67056080,+p4@ANKRD13D
Hg19::chr11:73097322..73097366,+p@chr11:73097322..73097366
+
Hg19::chr12:110888103..110888172,-p1@ARPC3
Hg19::chr15:40600028..40600061,-p2@PLCB2
Hg19::chr15:85259803..85259821,+p@chr15:85259803..85259821
+
Hg19::chr16:50059183..50059199,+p2@TMEM188
Hg19::chr17:38480637..38480649,+p@chr17:38480637..38480649
+
Hg19::chr17:43487729..43487738,-p1@uc002iiy.1
Hg19::chr17:72462766..72462831,+p1@CD300A
Hg19::chr19:18508396..18508460,-p1@LRRC25
Hg19::chr19:51920837..51920848,-p3@SIGLEC10
Hg19::chr19:51920861..51920864,-p6@SIGLEC10
Hg19::chr19:51920873..51920906,-p1@SIGLEC10
Hg19::chr19:51920954..51920971,-p2@SIGLEC10
Hg19::chr19:55084417..55084428,+p4@LILRA2
Hg19::chr1:236028436..236028467,-p@chr1:236028436..236028467
-
Hg19::chr1:244979057..244979081,+p@chr1:244979057..244979081
+
Hg19::chr20:1472009..1472020,-p4@SIRPB2
Hg19::chr20:1472029..1472032,-p5@SIRPB2
Hg19::chr20:48892848..48892884,+p1@ENST00000422459
Hg19::chr20:55950074..55950095,+p@chr20:55950074..55950095
+
Hg19::chr20:62708506..62708524,-p9@RGS19
Hg19::chr20:62710772..62710783,-p4@RGS19
Hg19::chr22:44577612..44577668,+p1@PARVG
Hg19::chr22:50968798..50968830,+p@chr22:50968798..50968830
+
Hg19::chr22:50968897..50968915,+p@chr22:50968897..50968915
+
Hg19::chr2:20624862..20624875,+p@chr2:20624862..20624875
+
Hg19::chr2:45795104..45795144,-p2@SRBD1
Hg19::chr3:72149553..72149577,-p1@ENST00000468646
p1@uc003dpb.1
Hg19::chr4:154387777..154387789,+p@chr4:154387777..154387789
+
Hg19::chr5:176735063..176735088,-p2@MXD3
Hg19::chr5:180229951..180229996,+p@chr5:180229951..180229996
+
Hg19::chr6:167370025..167370046,-p1@RNASET2
Hg19::chr6:42897260..42897305,+p2@CNPY3
Hg19::chr7:106505807..106505839,+p3@PIK3CG
Hg19::chr7:139529081..139529084,+p6@TBXAS1
Hg19::chr7:139529085..139529115,+p2@TBXAS1
Hg19::chr7:26331470..26331517,+p2@SNX10
Hg19::chr7:99750250..99750284,+p6@C7orf59
Hg19::chr9:130540938..130540952,-p2@SH2D3C


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

No GOStat results

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
hematopoietic stem cell5.16e-73168
angioblastic mesenchymal cell5.16e-73168
myeloid leukocyte5.33e-6972
leukocyte6.23e-68136
hematopoietic oligopotent progenitor cell9.37e-68161
hematopoietic multipotent progenitor cell9.37e-68161
hematopoietic cell3.34e-67177
myeloid cell3.87e-66108
common myeloid progenitor3.87e-66108
granulocyte monocyte progenitor cell1.34e-6167
macrophage dendritic cell progenitor1.22e-5861
monopoietic cell6.91e-5759
monocyte6.91e-5759
monoblast6.91e-5759
promonocyte6.91e-5759
myeloid lineage restricted progenitor cell2.56e-5666
nongranular leukocyte2.13e-55115
hematopoietic lineage restricted progenitor cell1.47e-54120
defensive cell6.10e-5148
phagocyte6.10e-5148
classical monocyte1.08e-4742
CD14-positive, CD16-negative classical monocyte1.08e-4742
stuff accumulating cell9.05e-2087
mesenchymal cell1.25e-14354
connective tissue cell1.05e-13361
intermediate monocyte4.51e-129
CD14-positive, CD16-positive monocyte4.51e-129
granulocyte5.10e-118
motile cell1.56e-10386
blood cell2.40e-0711
multi fate stem cell6.35e-07427
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.88e-6598
blood island8.88e-6598
hemolymphoid system2.60e-59108
bone marrow2.89e-5376
immune system2.00e-4893
bone element1.49e-4782
skeletal element3.78e-4190
skeletal system1.25e-34100
lateral plate mesoderm1.03e-19203
adult organism1.32e-14114
connective tissue6.58e-13371
musculoskeletal system1.26e-12167
blood5.63e-1115
haemolymphatic fluid5.63e-1115
organism substance5.63e-1115
mesoderm6.42e-07315
mesoderm-derived structure6.42e-07315
presumptive mesoderm6.42e-07315
Disease
Ontology termp-valuen
myeloid leukemia6.95e-0731


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)
MA0003.12.97219
MA0004.10.404373
MA0006.10.0559723
MA0007.11.45738
MA0009.10.309236
MA0014.10.79588
MA0017.10.648923
MA0019.10.713554
MA0024.10.234026
MA0025.10.413966
MA0027.11.81465
MA0028.12.02874
MA0029.10.24734
MA0030.10.672868
MA0031.10.571644
MA0038.10.294316
MA0040.11.29537
MA0041.10.768443
MA0042.11.04665
MA0043.10.309473
MA0046.10.301098
MA0048.10.816717
MA0050.10.381055
MA0051.11.5073
MA0052.10.707023
MA0055.10.835785
MA0056.10
MA0057.10.423246
MA0058.10.240697
MA0059.10.452115
MA0060.10.198625
MA0061.10.586938
MA0063.10
MA0066.10.294839
MA0067.10.570397
MA0068.10.568859
MA0069.10.298233
MA0070.10.289965
MA0071.10.248466
MA0072.10.286664
MA0073.11.04908
MA0074.11.01239
MA0076.11.57622
MA0077.10.281032
MA0078.10.418758
MA0081.12.41991
MA0083.10.845316
MA0084.10.739331
MA0087.10.284873
MA0088.10.244642
MA0089.10
MA0090.10.289076
MA0091.10.409312
MA0092.10.340194
MA0093.10.31174
MA0095.10
MA0098.10
MA0100.10.0935814
MA0101.10.538909
MA0103.10.0510613
MA0105.10.152006
MA0106.10.704738
MA0107.10.513551
MA0108.20.566954
MA0109.10
MA0111.10.311824
MA0113.11.21705
MA0114.10.7289
MA0115.10.50405
MA0116.14.13121
MA0117.10.337847
MA0119.10.214757
MA0122.10.941347
MA0124.10.468805
MA0125.10.399431
MA0130.10
MA0131.11.40489
MA0132.10
MA0133.10
MA0135.10.332279
MA0136.11.05099
MA0139.10.219459
MA0140.10.0698149
MA0141.10.447779
MA0142.10.176637
MA0143.10.742572
MA0144.10.063455
MA0145.11.88419
MA0146.12.17879
MA0147.10.187824
MA0148.11.68086
MA0149.10.0660182
MA0062.23.6393
MA0035.20.24463
MA0039.22.94509
MA0138.22.62117
MA0002.22.64857
MA0137.20.0690027
MA0104.20.100671
MA0047.20.100739
MA0112.21.49771
MA0065.21.16491
MA0150.10.279387
MA0151.10
MA0152.10.072456
MA0153.10.385866
MA0154.11.26547
MA0155.12.19971
MA0156.12.10041
MA0157.10.483135
MA0158.10
MA0159.10.340829
MA0160.10.482489
MA0161.10
MA0162.10.250989
MA0163.10.721272
MA0164.10.384671
MA0080.22.88326
MA0018.20.107308
MA0099.20.072601
MA0079.20.614559
MA0102.20.773745
MA0258.10.862122
MA0259.10.572972
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
EBF1#1879122.544704813305430.001731100097627140.010656275085234
ELF1#1997252.534582118337826.20505328922612e-072.8448180881189e-05
MAX#4149131.997219562311730.008989734168348840.0340840356787986
POLR2A#5430361.840674151335491.58595236861894e-078.8010244115937e-06
POU2F2#5452112.384937253218280.004681702869844110.0220905559782981
SPI1#6688275.274207969764613.13703166424514e-155.62935481068898e-13



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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