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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:26, 17 September 2013


Full id: C602_Macrophage_Monocytederived_CD14_Mast_Dendritic_lung_adipose



Phase1 CAGE Peaks

Hg19::chr18:43409037..43409056,+p2@SIGLEC15
Hg19::chr1:46008415..46008441,-p@chr1:46008415..46008441
-
Hg19::chr2:217259800..217259818,+p@chr2:217259800..217259818
+
Hg19::chr2:85636928..85636947,-p4@CAPG
Hg19::chr2:85637459..85637495,-p2@CAPG
Hg19::chr2:85637502..85637513,-p5@CAPG
Hg19::chr3:188664953..188664966,+p12@TPRG1
Hg19::chr3:188664988..188665018,+p6@TPRG1
Hg19::chr7:47520822..47520831,-p@chr7:47520822..47520831
-
Hg19::chr7:47520869..47520899,-p3@TNS3
Hg19::chr7:47520910..47520921,-p15@TNS3
Hg19::chr8:16050142..16050168,-p1@MSR1
Hg19::chr8:16050214..16050227,-p2@MSR1
Hg19::chr8:87111104..87111113,+p3@ATP6V0D2
Hg19::chr8:87111117..87111122,+p4@ATP6V0D2


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><br>

Cell Type
Ontology termp-valuen
macrophage dendritic cell progenitor4.72e-8461
monopoietic cell8.96e-8459
monocyte8.96e-8459
monoblast8.96e-8459
promonocyte8.96e-8459
granulocyte monocyte progenitor cell2.32e-7867
defensive cell9.54e-7748
phagocyte9.54e-7748
myeloid lineage restricted progenitor cell1.67e-7666
myeloid leukocyte5.99e-7572
classical monocyte1.29e-6242
CD14-positive, CD16-negative classical monocyte1.29e-6242
myeloid cell4.47e-49108
common myeloid progenitor4.47e-49108
nongranular leukocyte1.19e-39115
hematopoietic lineage restricted progenitor cell4.65e-39120
leukocyte1.95e-37136
stuff accumulating cell1.64e-3687
hematopoietic oligopotent progenitor cell3.20e-29161
hematopoietic multipotent progenitor cell3.20e-29161
hematopoietic stem cell1.19e-28168
angioblastic mesenchymal cell1.19e-28168
hematopoietic cell2.07e-26177
macrophage1.31e-156
adult endothelial progenitor cell1.49e-083
immature conventional dendritic cell9.97e-075
common dendritic progenitor9.97e-075
Uber Anatomy
Ontology termp-valuen
bone marrow3.35e-7076
immune system4.81e-6793
bone element5.35e-6482
hematopoietic system9.32e-6398
blood island9.32e-6398
hemolymphoid system9.37e-58108
skeletal element5.27e-5790
skeletal system7.90e-50100
musculoskeletal system2.76e-26167
lateral plate mesoderm2.08e-25203
mesoderm1.46e-15315
mesoderm-derived structure1.46e-15315
presumptive mesoderm1.46e-15315
organ3.50e-11503
adult organism7.08e-09114
developing anatomical structure1.55e-08581
germ layer1.66e-08560
germ layer / neural crest1.66e-08560
embryonic tissue1.66e-08560
presumptive structure1.66e-08560
germ layer / neural crest derived structure1.66e-08560
epiblast (generic)1.66e-08560
embryonic structure2.63e-08564
embryo5.26e-08592
anatomical system4.22e-07624
anatomical group4.66e-07625


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)
MA0003.10.000385441
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.0332175
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.11.2891
MA0038.10.904297
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.00246981
MA0056.10
MA0057.10.0873069
MA0058.10.538866
MA0059.10.536577
MA0060.10.0671843
MA0061.12.17853
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.341559
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.15.77193
MA0074.10.337035
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.536866
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.244241
MA0089.10
MA0090.11.75658
MA0091.10.258318
MA0092.11.2087
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.861002
MA0103.10.131472
MA0105.10.376193
MA0106.10.37688
MA0107.10.650533
MA0108.20.515791
MA0109.10
MA0111.10.617603
MA0113.10.39123
MA0114.10.30732
MA0115.10.900969
MA0116.12.20924
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.11.49639
MA0141.10.533493
MA0142.10.489543
MA0143.10.391385
MA0144.11.00343
MA0145.11.04117
MA0146.10.00187713
MA0147.10.0991954
MA0148.10.276339
MA0149.10.807822
MA0062.20.0512998
MA0035.20.824687
MA0039.20.688994
MA0138.20.425279
MA0002.20.0612545
MA0137.20.465392
MA0104.20.0667907
MA0047.21.7084
MA0112.20.124752
MA0065.20.0514203
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.0723831
MA0155.10.0403226
MA0156.10.469333
MA0157.11.17385
MA0158.10
MA0159.10.327637
MA0160.10.786431
MA0161.10
MA0162.10.0243066
MA0163.10.0815692
MA0164.10.402162
MA0080.20.432036
MA0018.20.378086
MA0099.20.312108
MA0079.20.0966405
MA0102.21.1957
MA0258.10.0785319
MA0259.10.104286
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
POU5F1#5460367.08784029038111.16739030186779e-050.000297006274632814



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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