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{{Coexpression_clusters
{
|full_id=C2518_Neutrophils_CD14_Eosinophils_Natural_Basophils_Peripheral_CD8
 

Latest revision as of 12:07, 17 September 2013


Full id: C2518_Neutrophils_CD14_Eosinophils_Natural_Basophils_Peripheral_CD8



Phase1 CAGE Peaks

Hg19::chr1:12239267..12239284,-p@chr1:12239267..12239284
-
Hg19::chr21:36419687..36419698,+p@chr21:36419687..36419698
+
Hg19::chr21:36421074..36421093,-p@chr21:36421074..36421093
-
Hg19::chr21:36421097..36421121,-p@chr21:36421097..36421121
-


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
leukocyte1.51e-70136
hematopoietic stem cell7.87e-65168
angioblastic mesenchymal cell7.87e-65168
hematopoietic cell2.88e-64177
myeloid leukocyte5.95e-6472
hematopoietic lineage restricted progenitor cell2.05e-58120
hematopoietic oligopotent progenitor cell2.89e-58161
hematopoietic multipotent progenitor cell2.89e-58161
classical monocyte3.38e-5642
CD14-positive, CD16-negative classical monocyte3.38e-5642
nongranular leukocyte9.66e-56115
myeloid lineage restricted progenitor cell1.04e-5366
defensive cell1.85e-4948
phagocyte1.85e-4948
granulocyte monocyte progenitor cell1.04e-4867
myeloid cell1.83e-47108
common myeloid progenitor1.83e-47108
monopoietic cell4.38e-4659
monocyte4.38e-4659
monoblast4.38e-4659
promonocyte4.38e-4659
macrophage dendritic cell progenitor4.80e-4461
mesenchymal cell1.31e-21354
stuff accumulating cell1.32e-2187
connective tissue cell1.34e-20361
motile cell4.45e-17386
mature alpha-beta T cell5.11e-1618
alpha-beta T cell5.11e-1618
immature T cell5.11e-1618
mature T cell5.11e-1618
immature alpha-beta T cell5.11e-1618
stem cell2.59e-15441
T cell7.62e-1525
pro-T cell7.62e-1525
multi fate stem cell1.91e-14427
somatic stem cell2.49e-14433
granulocyte1.11e-138
intermediate monocyte1.56e-139
CD14-positive, CD16-positive monocyte1.56e-139
nucleate cell1.81e-1155
blood cell2.07e-1111
lymphoid lineage restricted progenitor cell1.44e-1052
lymphocyte3.10e-1053
common lymphoid progenitor3.10e-1053
CD4-positive, alpha-beta T cell8.17e-106
CD8-positive, alpha-beta T cell1.89e-0911
circulating cell2.30e-086
native cell2.28e-07722
histamine secreting cell4.34e-075
biogenic amine secreting cell4.34e-075
granulocytopoietic cell4.34e-075
mast cell4.34e-075
mast cell progenitor4.34e-075
basophil mast progenitor cell4.34e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.96e-5498
blood island1.96e-5498
hemolymphoid system2.69e-47108
bone marrow4.17e-4676
bone element2.24e-4182
immune system3.54e-4093
skeletal element1.43e-3790
skeletal system5.77e-32100
connective tissue3.14e-19371
lateral plate mesoderm1.19e-16203
musculoskeletal system2.64e-14167
mesoderm1.13e-07315
mesoderm-derived structure1.13e-07315
presumptive mesoderm1.13e-07315
blood1.62e-0715
haemolymphatic fluid1.62e-0715
organism substance1.62e-0715


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.20.0021048
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BATF#10538212.17890089615180.009566758805047810.0360194211341573
BCL11A#53335214.18472755180350.007108328585298740.0296255528600509
BCL3#602217.27355140186920.004834494208076070.0226752477027555
EBF1#187936.679850134926750.005184294118278910.0240480787661084
EP300#203335.08045629466740.01144298405398240.0418948962915889
FOS#235336.74846648167080.005032452776317940.0234667292720395
IRF4#3662210.95725634337210.01174530180688030.0428440353256532
POU2F2#545236.829593043306890.004860473775203740.0227623434199589



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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