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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0.042127323255851,

Latest revision as of 12:12, 17 September 2013


Full id: C2740_Mast_acute_small_leukemia_chronic_biphenotypic_adult



Phase1 CAGE Peaks

Hg19::chr3:42888864..42888881,+p@chr3:42888864..42888881
+
Hg19::chr4:79697338..79697350,+p10@BMP2K
Hg19::chr4:79697376..79697386,+p9@BMP2K
Hg19::chrX:155227410..155227421,+p4@IL9R


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:0004919interleukin-9 receptor activity0.00176616036736136
GO:0019983interleukin-9 binding0.00176616036736136
GO:0004907interleukin receptor activity0.035302931154496
GO:0019965interleukin binding0.035302931154496
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.048697238500048
GO:0019838growth factor binding0.0498850490643833
GO:0019955cytokine binding0.0498850490643833



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
myeloid cell1.56e-28108
common myeloid progenitor1.56e-28108
hematopoietic oligopotent progenitor cell8.10e-26161
hematopoietic multipotent progenitor cell8.10e-26161
hematopoietic stem cell4.71e-25168
angioblastic mesenchymal cell4.71e-25168
hematopoietic cell9.94e-23177
myeloid lineage restricted progenitor cell3.19e-1466
hematopoietic lineage restricted progenitor cell2.28e-13120
granulocyte monocyte progenitor cell6.00e-1367
myeloid leukocyte2.22e-1172
leukocyte5.44e-11136
histamine secreting cell1.01e-095
biogenic amine secreting cell1.01e-095
granulocytopoietic cell1.01e-095
mast cell1.01e-095
mast cell progenitor1.01e-095
basophil mast progenitor cell1.01e-095
macrophage dendritic cell progenitor5.63e-0961
monopoietic cell1.74e-0859
monocyte1.74e-0859
monoblast1.74e-0859
promonocyte1.74e-0859
nongranular leukocyte9.26e-08115
mesenchymal cell1.30e-07354
connective tissue cell4.23e-07361
defensive cell7.90e-0748
phagocyte7.90e-0748
Uber Anatomy
Ontology termp-valuen
immune system3.42e-1593
hemolymphoid system2.66e-13108
hematopoietic system6.90e-1398
blood island6.90e-1398
bone element1.06e-1182
bone marrow1.91e-1176
skeletal element7.64e-1090
adult organism2.32e-09114
skeletal system1.08e-08100
neural tube3.72e-0756
neural rod3.72e-0756
future spinal cord3.72e-0756
neural keel3.72e-0756
regional part of nervous system6.25e-0753
regional part of brain6.25e-0753
connective tissue9.22e-07371
Disease
Ontology termp-valuen
leukemia3.14e-2039
myeloid leukemia4.16e-1931
hematologic cancer1.23e-1751
immune system cancer1.23e-1751
chronic leukemia2.72e-078


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)
MA0003.10.720743
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.114.5548
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.13.24733
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
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
MA0145.10.569905
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.13.14178
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.29.35212
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
ATF3#467211.23158726300440.01119559039922220.041133337990022
CCNT2#90534.752151182721970.01386206996689490.0487356333829035
JUND#372735.245997956403270.01043432751748420.0387081565587516
NANOG#79923214.62238924050630.006698757715363760.028493933818062



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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