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Coexpression cluster:C2175: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 12:00, 17 September 2013


Full id: C2175_CD14_CD14CD16_splenic_migratory_Peripheral_Basophils_Whole



Phase1 CAGE Peaks

Hg19::chr12:10124110..10124121,+p2@CLEC12A
Hg19::chr4:38080384..38080414,+p@chr4:38080384..38080414
+
Hg19::chr5:54070798..54070804,+p@chr5:54070798..54070804
+
Hg19::chr9:136343729..136343751,-p4@SLC2A6


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:0005355glucose transmembrane transporter activity0.0164759143109795
GO:0015149hexose transmembrane transporter activity0.0164759143109795
GO:0015145monosaccharide transmembrane transporter activity0.0164759143109795
GO:0005351sugar:hydrogen ion symporter activity0.022368731471487
GO:0051119sugar transmembrane transporter activity0.022368731471487
GO:0015144carbohydrate transmembrane transporter activity0.022368731471487
GO:0008643carbohydrate transport0.022368731471487
GO:0015293symporter activity0.0425894721577773



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
monopoietic cell2.35e-8159
monocyte2.35e-8159
monoblast2.35e-8159
promonocyte2.35e-8159
myeloid leukocyte3.49e-7972
macrophage dendritic cell progenitor4.32e-7861
myeloid lineage restricted progenitor cell1.03e-7566
defensive cell1.00e-7448
phagocyte1.00e-7448
granulocyte monocyte progenitor cell2.66e-7467
classical monocyte2.97e-6942
CD14-positive, CD16-negative classical monocyte2.97e-6942
leukocyte7.17e-66136
nongranular leukocyte3.93e-63115
myeloid cell9.13e-57108
common myeloid progenitor9.13e-57108
hematopoietic lineage restricted progenitor cell1.03e-56120
hematopoietic stem cell6.69e-53168
angioblastic mesenchymal cell6.69e-53168
hematopoietic oligopotent progenitor cell4.86e-51161
hematopoietic multipotent progenitor cell4.86e-51161
hematopoietic cell3.08e-50177
stuff accumulating cell2.26e-3587
intermediate monocyte1.49e-169
CD14-positive, CD16-positive monocyte1.49e-169
mesenchymal cell1.24e-14354
connective tissue cell6.82e-14361
motile cell8.03e-12386
multi fate stem cell3.38e-09427
stem cell3.59e-09441
somatic stem cell9.20e-09433
conventional dendritic cell1.57e-078
macrophage4.72e-076
non-classical monocyte8.67e-073
CD14-low, CD16-positive monocyte8.67e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.73e-7198
blood island2.73e-7198
hemolymphoid system6.82e-71108
immune system2.73e-6693
bone marrow2.91e-6376
bone element3.03e-5782
skeletal element1.80e-5090
skeletal system3.76e-45100
lateral plate mesoderm8.74e-29203
musculoskeletal system1.77e-20167
mesoderm1.20e-13315
mesoderm-derived structure1.20e-13315
presumptive mesoderm1.20e-13315
connective tissue2.00e-13371


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
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
MA0061.11.68681
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
MA0081.10.604638
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
MA0101.11.33363
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.12.98058
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
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
HNF4A#3172211.56614518147680.01057585681762490.0390625233475714



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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