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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0362496447385107,

Latest revision as of 11:57, 17 September 2013


Full id: C2049_CD14_Mast_Basophils_Eosinophils_Neutrophils_Peripheral_CD14CD16



Phase1 CAGE Peaks

Hg19::chr10:135122318..135122339,-p4@TUBGCP2
Hg19::chr11:62321037..62321046,-p@chr11:62321037..62321046
-
Hg19::chr14:55738772..55738777,-p2@ENST00000556183
Hg19::chr9:108007969..108007987,+p@chr9:108007969..108007987
+


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:0007020microtubule nucleation0.00376780878370423
GO:0005881cytoplasmic microtubule0.00376780878370423
GO:0000922spindle pole0.00973350602456925
GO:0005819spindle0.0183680678205581
GO:0000226microtubule cytoskeleton organization and biogenesis0.0192158247968915
GO:0005813centrosome0.0197809961144472
GO:0005815microtubule organizing center0.0197809961144472
GO:0005874microtubule0.0320263746614859
GO:0007017microtubule-based process0.0320263746614859
GO:0006461protein complex assembly0.0320263746614859
GO:0015630microtubule cytoskeleton0.0442717532085247



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 monocyte5.70e-5042
CD14-positive, CD16-negative classical monocyte5.70e-5042
leukocyte2.28e-44136
myeloid leukocyte1.75e-4372
defensive cell8.72e-4248
phagocyte8.72e-4248
granulocyte monocyte progenitor cell3.05e-4167
macrophage dendritic cell progenitor4.90e-3861
myeloid lineage restricted progenitor cell6.54e-3866
monopoietic cell1.47e-3559
monocyte1.47e-3559
monoblast1.47e-3559
promonocyte1.47e-3559
hematopoietic lineage restricted progenitor cell5.91e-34120
hematopoietic stem cell3.51e-32168
angioblastic mesenchymal cell3.51e-32168
nongranular leukocyte9.17e-32115
myeloid cell1.80e-29108
common myeloid progenitor1.80e-29108
hematopoietic cell2.91e-29177
hematopoietic oligopotent progenitor cell1.23e-28161
hematopoietic multipotent progenitor cell1.23e-28161
stuff accumulating cell6.26e-2187
intermediate monocyte4.81e-149
CD14-positive, CD16-positive monocyte4.81e-149
mesenchymal cell2.39e-10354
connective tissue cell1.10e-09361
motile cell6.94e-09386
Langerhans cell1.63e-075
dendritic cell3.47e-0710
conventional dendritic cell4.36e-078
Uber Anatomy
Ontology termp-valuen
bone marrow5.70e-3676
bone element4.59e-3282
hematopoietic system3.25e-2898
blood island3.25e-2898
skeletal element1.09e-2790
immune system2.24e-2793
hemolymphoid system5.82e-25108
skeletal system3.08e-23100
musculoskeletal system7.04e-09167
lateral plate mesoderm8.09e-09203
connective tissue8.52e-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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.13.08565
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
MA0048.10.709734
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
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
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
MA0105.11.22348
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
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.65877
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.11.07498
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
BRCA1#672210.09211532161190.0137713969900260.0484576304788021
CCNT2#90534.752151182721970.01386206996689490.0486979287992375
GATA3#2625213.6182581786030.00769665208093340.0316842982530786
JUND#372735.245997956403270.01043432751748420.0386600940683459
RFX5#599339.035933120396320.002144561191324070.0123791425557229
TAF1#687243.343046285745290.008005664898701650.0321047358735745



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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