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{{Coexpression_clusters
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|full_id=C3607_Dendritic_CD8_CD4_Macrophage_Monocytederived_chronic_Melanocyte
|id=C3607
}}

Latest revision as of 12:29, 17 September 2013


Full id: C3607_Dendritic_CD8_CD4_Macrophage_Monocytederived_chronic_Melanocyte



Phase1 CAGE Peaks

Hg19::chr17:16319065..16319082,+p4@TRPV2
Hg19::chr17:16319083..16319126,+p2@TRPV2
Hg19::chr1:2487631..2487646,+p7@TNFRSF14


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:0005031tumor necrosis factor receptor activity0.0147160534274282
GO:0043120tumor necrosis factor binding0.0147160534274282
GO:0005035death receptor activity0.0147160534274282
GO:0005887integral to plasma membrane0.0213323094237266
GO:0031226intrinsic to plasma membrane0.0213323094237266
GO:0009266response to temperature stimulus0.0213323094237266
GO:0044459plasma membrane part0.0406706632532928
GO:0048770pigment granule0.0406706632532928
GO:0042470melanosome0.0406706632532928
GO:0019955cytokine binding0.0436494179313354
GO:0005262calcium channel activity0.0476836500583188



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell4.71e-59168
angioblastic mesenchymal cell4.71e-59168
hematopoietic cell8.66e-59177
leukocyte1.41e-55136
hematopoietic oligopotent progenitor cell2.26e-55161
hematopoietic multipotent progenitor cell2.26e-55161
nongranular leukocyte6.60e-47115
hematopoietic lineage restricted progenitor cell7.04e-47120
connective tissue cell1.43e-34361
mesenchymal cell4.59e-34354
multi fate stem cell4.43e-33427
myeloid cell4.08e-32108
common myeloid progenitor4.08e-32108
somatic stem cell1.92e-30433
stem cell4.07e-30441
motile cell8.93e-29386
myeloid leukocyte5.14e-2872
granulocyte monocyte progenitor cell8.71e-2767
myeloid lineage restricted progenitor cell1.41e-2466
macrophage dendritic cell progenitor4.48e-2461
monopoietic cell1.26e-2359
monocyte1.26e-2359
monoblast1.26e-2359
promonocyte1.26e-2359
lymphoid lineage restricted progenitor cell1.35e-2052
lymphocyte1.44e-2053
common lymphoid progenitor1.44e-2053
defensive cell1.15e-1948
phagocyte1.15e-1948
nucleate cell3.68e-1955
classical monocyte3.45e-1642
CD14-positive, CD16-negative classical monocyte3.45e-1642
T cell4.54e-1325
pro-T cell4.54e-1325
mature alpha-beta T cell3.14e-1218
alpha-beta T cell3.14e-1218
immature T cell3.14e-1218
mature T cell3.14e-1218
immature alpha-beta T cell3.14e-1218
somatic cell4.43e-10588
stuff accumulating cell5.66e-1087
CD8-positive, alpha-beta T cell1.88e-0811
lymphocyte of B lineage1.45e-0724
pro-B cell1.45e-0724
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.36e-37108
hematopoietic system1.03e-3698
blood island1.03e-3698
connective tissue3.30e-32371
immune system1.44e-3093
bone marrow6.69e-2776
lateral plate mesoderm1.42e-22203
bone element8.70e-2282
skeletal element1.10e-1890
skeletal system3.63e-15100
musculoskeletal system8.63e-13167
mesoderm9.31e-13315
mesoderm-derived structure9.31e-13315
presumptive mesoderm9.31e-13315
blood2.56e-0715
haemolymphatic fluid2.56e-0715
organism substance2.56e-0715
Disease
Ontology termp-valuen
hematologic cancer7.89e-0851
immune system cancer7.89e-0851


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.79391
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
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.11.52002
MA0105.11.5295
MA0106.10.986396
MA0107.11.36919
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
MA0145.11.37817
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
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
EGR1#195834.988179094810140.008056488137383440.0320135283103219



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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