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{{Coexpression_clusters
{
|full_id=C3725_CD14_CD4_CD8_Burkitt_CD19_Basophils_lymphoma
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Latest revision as of 12:31, 17 September 2013


Full id: C3725_CD14_CD4_CD8_Burkitt_CD19_Basophils_lymphoma



Phase1 CAGE Peaks

Hg19::chr18:48405033..48405061,+p3@ME2
Hg19::chr4:110481348..110481368,+p2@CCDC109B
Hg19::chr4:110481374..110481458,+p1@CCDC109B


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:0016619malate dehydrogenase (oxaloacetate-decarboxylating) activity0.00129518426939833
GO:0004471malate dehydrogenase (decarboxylating) activity0.00129518426939833
GO:0004470malic enzyme activity0.00518005080645473
GO:0006108malate metabolic process0.00518005080645473
GO:0016615malate dehydrogenase activity0.00518005080645473
GO:0043648dicarboxylic acid metabolic process0.00690612438981643
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.0118362817252174
GO:0051287NAD binding0.0232889542237499
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0393973010196954
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0393973010196954
GO:0031980mitochondrial lumen0.0393973010196954
GO:0005759mitochondrial matrix0.0393973010196954



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
nongranular leukocyte3.43e-45115
hematopoietic lineage restricted progenitor cell4.54e-41120
leukocyte6.57e-39136
hematopoietic stem cell1.28e-31168
angioblastic mesenchymal cell1.28e-31168
hematopoietic oligopotent progenitor cell1.45e-28161
hematopoietic multipotent progenitor cell1.45e-28161
hematopoietic cell5.02e-27177
defensive cell6.75e-2648
phagocyte6.75e-2648
classical monocyte2.20e-2542
CD14-positive, CD16-negative classical monocyte2.20e-2542
nucleate cell1.56e-2255
lymphocyte2.00e-2253
common lymphoid progenitor2.00e-2253
lymphoid lineage restricted progenitor cell5.08e-2252
monopoietic cell2.85e-2059
monocyte2.85e-2059
monoblast2.85e-2059
promonocyte2.85e-2059
macrophage dendritic cell progenitor5.70e-2061
myeloid lineage restricted progenitor cell7.23e-1966
granulocyte monocyte progenitor cell7.28e-1967
myeloid leukocyte4.89e-1672
stem cell9.42e-13441
somatic stem cell1.43e-12433
multi fate stem cell1.66e-12427
native cell2.00e-12722
lymphocyte of B lineage6.83e-1224
pro-B cell6.83e-1224
mesenchymal cell5.42e-11354
somatic cell8.57e-11588
T cell4.65e-1025
pro-T cell4.65e-1025
stuff accumulating cell5.40e-1087
myeloid cell1.02e-09108
common myeloid progenitor1.02e-09108
mature alpha-beta T cell1.06e-0918
alpha-beta T cell1.06e-0918
immature T cell1.06e-0918
mature T cell1.06e-0918
immature alpha-beta T cell1.06e-0918
connective tissue cell1.58e-09361
motile cell2.48e-09386
B cell6.03e-0914
animal cell3.64e-07679
eukaryotic cell3.64e-07679
meso-epithelial cell4.77e-0745
CD8-positive, alpha-beta T cell7.86e-0711
endothelial cell of vascular tree8.45e-0724
endothelial cell9.23e-0736
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.48e-25108
hematopoietic system2.23e-2398
blood island2.23e-2398
immune system1.34e-2293
bone marrow4.15e-1876
bone element9.66e-1782
lateral plate mesoderm6.34e-16203
skeletal element3.51e-1490
skeletal system3.71e-13100
connective tissue2.83e-09371
musculoskeletal system1.63e-08167
mesoderm1.46e-07315
mesoderm-derived structure1.46e-07315
presumptive mesoderm1.46e-07315


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
ELF1#199734.258097958807540.01295179875054610.046204157320272
ZNF263#1012738.221841637010680.001799043925565870.0109359378698664



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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