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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2740_Mast_acute_small_leukemia_chronic_biphenotypic_adult
|full_id=C2740_Mast_acute_small_leukemia_chronic_biphenotypic_adult
|gostat_on_coexpression_clusters=GO:0004919!interleukin-9 receptor activity!0.00176616036736136!3581$GO:0019983!interleukin-9 binding!0.00176616036736136!3581$GO:0004907!interleukin receptor activity!0.035302931154496!3581$GO:0019965!interleukin binding!0.035302931154496!3581$GO:0004896!hematopoietin/interferon-class (D200-domain) cytokine receptor activity!0.048697238500048!3581$GO:0019838!growth factor binding!0.0498850490643833!3581$GO:0019955!cytokine binding!0.0498850490643833!3581
|gostat_on_coexpression_clusters=GO:0004919!interleukin-9 receptor activity!0.00176616036736136!3581$GO:0019983!interleukin-9 binding!0.00176616036736136!3581$GO:0004907!interleukin receptor activity!0.035302931154496!3581$GO:0019965!interleukin binding!0.035302931154496!3581$GO:0004896!hematopoietin/interferon-class (D200-domain) cytokine receptor activity!0.048697238500048!3581$GO:0019838!growth factor binding!0.0498850490643833!3581$GO:0019955!cytokine binding!0.0498850490643833!3581

Revision as of 15:31, 12 September 2012


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
hematopoietic oligopotent progenitor cell4.37e-31165
hematopoietic multipotent progenitor cell4.37e-31165
myeloid cell1.31e-30112
common myeloid progenitor1.31e-30112
hematopoietic stem cell2.69e-30172
angioblastic mesenchymal cell2.69e-30172
hematopoietic cell2.52e-27182
hematopoietic lineage restricted progenitor cell1.41e-16124
leukocyte2.94e-16140
granulocyte monocyte progenitor cell2.61e-1571
myeloid lineage restricted progenitor cell1.31e-1470
myeloid leukocyte7.55e-1476
nongranular leukocyte3.35e-12119
macrophage dendritic cell progenitor1.12e-1165
monopoietic cell1.23e-1063
monocyte1.23e-1063
monoblast1.23e-1063
promonocyte1.23e-1063
CD14-positive, CD16-negative classical monocyte2.38e-0842
mesenchymal cell7.14e-08358
connective tissue cell3.04e-07365
classical monocyte4.12e-0745
Uber Anatomy
Ontology termp-valuen
hemolymphoid system5.90e-18112
hematopoietic system5.16e-16102
blood island5.16e-16102
immune system2.07e-15115
adult organism1.01e-14115
bone marrow1.47e-1380
bone element2.42e-1386
neural tube7.92e-1057
neural rod7.92e-1057
future spinal cord7.92e-1057
neural keel7.92e-1057
skeletal element4.35e-09101
skeletal system4.35e-09101
central nervous system1.22e-0882
regional part of brain1.32e-0859
brain2.65e-0869
future brain2.65e-0869
regional part of forebrain3.34e-0841
forebrain3.34e-0841
future forebrain3.34e-0841
telencephalon5.13e-0834
anterior neural tube9.02e-0842
gray matter1.58e-0734
brain grey matter1.58e-0734
regional part of telencephalon1.74e-0733
cerebral hemisphere7.06e-0732
Disease
Ontology termp-valuen
leukemia9.13e-2139
hematologic cancer1.08e-2051
immune system cancer1.08e-2051
myeloid leukemia5.28e-1731


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)

{{{tfbs_overrepresentation_jaspar}}}



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.