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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0943422368253682

Latest revision as of 11:32, 17 September 2013


Full id: C842_Neutrophils_CD14CD16_CD14_Eosinophils_migratory_Mesenchymal_Fibroblast



Phase1 CAGE Peaks

Hg19::chr16:84600281..84600315,-p@chr16:84600281..84600315
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Hg19::chr16:84600344..84600356,-p@chr16:84600344..84600356
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Hg19::chr16:84600375..84600405,-p@chr16:84600375..84600405
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Hg19::chr16:84600432..84600461,-p@chr16:84600432..84600461
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Hg19::chr16:84600468..84600488,-p@chr16:84600468..84600488
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Hg19::chr16:84623794..84623816,-p3@COTL1
Hg19::chr16:84623843..84623875,-p4@COTL1
Hg19::chr16:84651647..84651667,-p2@COTL1
Hg19::chr16:84651673..84651691,-p1@COTL1
Hg19::chr3:50294928..50294962,+p1@AY555145


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:0031280negative regulation of cyclase activity0.0155978685153231
GO:0007194negative regulation of adenylate cyclase activity0.0155978685153231
GO:0051350negative regulation of lyase activity0.0155978685153231
GO:0045761regulation of adenylate cyclase activity0.0187100024153625
GO:0007584response to nutrient0.0187100024153625
GO:0031279regulation of cyclase activity0.0187100024153625
GO:0051339regulation of lyase activity0.0187100024153625
GO:0031667response to nutrient levels0.0225929366485817
GO:0009991response to extracellular stimulus0.0225929366485817
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0225929366485817
GO:0019933cAMP-mediated signaling0.0225929366485817
GO:0043086negative regulation of catalytic activity0.0225929366485817
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0271420350435088
GO:0019935cyclic-nucleotide-mediated signaling0.0271420350435088



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
somatic cell4.79e-31588
defensive cell5.39e-2848
phagocyte5.39e-2848
myeloid leukocyte3.36e-2772
native cell9.80e-27722
classical monocyte1.92e-2642
CD14-positive, CD16-negative classical monocyte1.92e-2642
animal cell3.07e-25679
eukaryotic cell3.07e-25679
monopoietic cell7.87e-2559
monocyte7.87e-2559
monoblast7.87e-2559
promonocyte7.87e-2559
macrophage dendritic cell progenitor9.97e-2361
multi fate stem cell3.37e-22427
somatic stem cell1.26e-21433
myeloid lineage restricted progenitor cell7.10e-2166
granulocyte monocyte progenitor cell1.98e-2067
stem cell2.12e-20441
mesodermal cell2.20e-17121
stuff accumulating cell7.85e-1687
leukocyte2.21e-14136
myeloid cell3.11e-13108
common myeloid progenitor3.11e-13108
nongranular leukocyte3.58e-13115
connective tissue cell2.06e-12361
mesenchymal cell1.38e-11354
contractile cell1.18e-1059
muscle precursor cell3.73e-1058
myoblast3.73e-1058
multi-potent skeletal muscle stem cell3.73e-1058
hematopoietic lineage restricted progenitor cell3.81e-10120
muscle cell8.21e-1055
smooth muscle cell3.26e-0943
smooth muscle myoblast3.26e-0943
electrically responsive cell4.40e-0961
electrically active cell4.40e-0961
motile cell1.58e-08386
hematopoietic oligopotent progenitor cell3.02e-08161
hematopoietic multipotent progenitor cell3.02e-08161
vascular associated smooth muscle cell4.52e-0832
lining cell5.11e-0858
barrier cell5.11e-0858
hematopoietic stem cell1.35e-07168
angioblastic mesenchymal cell1.35e-07168
embryonic cell3.09e-07250
hematopoietic cell5.35e-07177
Uber Anatomy
Ontology termp-valuen
musculoskeletal system8.93e-23167
mesoderm1.88e-21315
mesoderm-derived structure1.88e-21315
presumptive mesoderm1.88e-21315
lateral plate mesoderm3.65e-21203
hemolymphoid system2.66e-19108
bone marrow3.04e-1876
hematopoietic system4.53e-1898
blood island4.53e-1898
immune system1.38e-1793
skeletal element2.14e-1590
bone element3.85e-1582
skeletal system6.41e-15100
epithelial vesicle3.26e-1278
connective tissue1.61e-10371
cardiovascular system6.19e-10109
somite1.27e-0971
presomitic mesoderm1.27e-0971
presumptive segmental plate1.27e-0971
dermomyotome1.27e-0971
trunk paraxial mesoderm1.27e-0971
paraxial mesoderm2.34e-0972
presumptive paraxial mesoderm2.34e-0972
multilaminar epithelium2.80e-0983
dense mesenchyme tissue3.02e-0973
vasculature5.46e-0978
vascular system5.46e-0978
circulatory system9.55e-09112
skeletal muscle tissue6.90e-0862
striated muscle tissue6.90e-0862
myotome6.90e-0862
artery1.88e-0742
arterial blood vessel1.88e-0742
arterial system1.88e-0742
vessel2.38e-0768
muscle tissue2.75e-0764
musculature2.75e-0764
musculature of body2.75e-0764


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)
MA0003.10.1987
MA0004.10.990587
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.462516
MA0017.10.270554
MA0019.10.520264
MA0024.11.7227
MA0025.10.960689
MA0027.12.43535
MA0028.10.697761
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.11.19169
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.46253
MA0058.10.293055
MA0059.10.291897
MA0060.12.65966
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.11.56182
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.16.11061
MA0074.10.4723
MA0076.10.828432
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.918839
MA0093.11.2478
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.0508589
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.12.16975
MA0130.10
MA0131.11.43152
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.945459
MA0146.10.243477
MA0147.10.184931
MA0148.11.04145
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.233545
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.20.428616
MA0047.21.25985
MA0112.20.133417
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.16.96763
MA0155.10.866026
MA0156.10.257809
MA0157.11.4867
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.11.23231
MA0163.10.0235237
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.22.25774
MA0102.23.02887
MA0258.10.155735
MA0259.10.191914
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
SP1#666773.988866964698630.0003734365591501510.00371193878377107



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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