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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0.552571649267773,

Latest revision as of 11:28, 17 September 2013


Full id: C658_Monocytederived_CD4_mycosis_Whole_Neutrophils_mucinous_lymph



Phase1 CAGE Peaks

Hg19::chr11:73685878..73685921,+p1@CU680035
Hg19::chr11:73685925..73685959,-p@chr11:73685925..73685959
-
Hg19::chr11:73685992..73686067,-p@chr11:73685992..73686067
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Hg19::chr11:73686080..73686092,-p@chr11:73686080..73686092
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Hg19::chr11:73686156..73686172,-p@chr11:73686156..73686172
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Hg19::chr11:73686574..73686614,-p@chr11:73686574..73686614
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Hg19::chr11:73686645..73686687,-p@chr11:73686645..73686687
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Hg19::chr11:73687727..73687743,-p@chr11:73687727..73687743
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Hg19::chr11:73687776..73687798,-p@chr11:73687776..73687798
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Hg19::chr11:73687914..73687931,-p6@UCP2
Hg19::chr11:73687932..73687955,-p4@UCP2
Hg19::chr11:73687967..73687985,-p7@UCP2
Hg19::chr11:73687997..73688019,-p5@UCP2


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:0000303response to superoxide0.00345873071941599
GO:0000305response to oxygen radical0.00345873071941599
GO:0000302response to reactive oxygen species0.0124514305898976
GO:0006839mitochondrial transport0.0166019074531967
GO:0007005mitochondrion organization and biogenesis0.0233464323560579
GO:0006979response to oxidative stress0.0233464323560579
GO:0015992proton transport0.0233464323560579
GO:0006818hydrogen transport0.0233464323560579
GO:0005743mitochondrial inner membrane0.0457935947250677
GO:0019866organelle inner membrane0.0457935947250677
GO:0031966mitochondrial membrane0.0498057223595903
GO:0005740mitochondrial envelope0.0498057223595903



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 cell3.58e-51168
angioblastic mesenchymal cell3.58e-51168
hematopoietic cell4.56e-51177
hematopoietic oligopotent progenitor cell1.81e-47161
hematopoietic multipotent progenitor cell1.81e-47161
leukocyte1.85e-43136
hematopoietic lineage restricted progenitor cell6.69e-40120
nongranular leukocyte3.47e-39115
myeloid cell1.40e-27108
common myeloid progenitor1.40e-27108
myeloid lineage restricted progenitor cell4.19e-2166
granulocyte monocyte progenitor cell7.83e-2067
macrophage dendritic cell progenitor1.20e-1961
myeloid leukocyte1.51e-1972
nucleate cell3.08e-1955
monopoietic cell7.15e-1959
monocyte7.15e-1959
monoblast7.15e-1959
promonocyte7.15e-1959
lymphocyte7.31e-1853
common lymphoid progenitor7.31e-1853
lymphoid lineage restricted progenitor cell3.17e-1752
defensive cell2.04e-1548
phagocyte2.04e-1548
classical monocyte1.10e-1142
CD14-positive, CD16-negative classical monocyte1.10e-1142
lymphocyte of B lineage1.57e-1024
pro-B cell1.57e-1024
stuff accumulating cell6.09e-0987
T cell1.80e-0725
pro-T cell1.80e-0725
B cell7.91e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.37e-2598
blood island4.37e-2598
hemolymphoid system2.41e-21108
bone marrow4.35e-1676
immune system1.72e-1593
bone element1.19e-1382
skeletal element1.95e-1090
skeletal system1.41e-08100
blood1.16e-0715
haemolymphatic fluid1.16e-0715
organism substance1.16e-0715
Disease
Ontology termp-valuen
hematologic cancer1.43e-1251
immune system cancer1.43e-1251
leukemia3.04e-0939
myeloid leukemia2.32e-0731


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)
MA0003.10.014173
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.11.72147
MA0014.10.000874969
MA0017.11.72263
MA0019.11.09485
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.11.00626
MA0040.11.56266
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.30948
MA0050.11.4276
MA0051.10.383704
MA0052.10.652145
MA0055.10.3329
MA0056.10
MA0057.10.0301256
MA0058.10.219229
MA0059.10.623149
MA0060.10.0892161
MA0061.10.0732084
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.0529803
MA0069.10.710614
MA0070.11.66969
MA0071.10.35315
MA0072.10.695528
MA0073.15.08229e-05
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.12.07344
MA0081.11.16979
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.11.58454
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.948111
MA0105.10.26318
MA0106.10.424592
MA0107.10.121572
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.11.80492
MA0115.13.61882
MA0116.10.123927
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.0663461
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.11.72258
MA0145.11.70801
MA0146.11.75468
MA0147.10.126316
MA0148.10.319209
MA0149.15.45299
MA0062.20.0702147
MA0035.20.350194
MA0039.20.00699112
MA0138.20.474787
MA0002.22.64652
MA0137.21.04503
MA0104.20.088751
MA0047.20.413608
MA0112.20.355033
MA0065.20.953721
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.0246626
MA0155.11.18433
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.11.29394
MA0160.10.332385
MA0161.10
MA0162.10.0446668
MA0163.10.00707238
MA0164.10.450848
MA0080.20.511865
MA0018.20.425847
MA0099.20.356906
MA0079.20.00408349
MA0102.21.25596
MA0258.10.685719
MA0259.10.132107
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
POLR2A#5430121.982264470668990.0007703649959180760.00604161221060959



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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