Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Classifying leukemia types with chromatin conformation data

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE55408 | GEO | 2014/02/27

SECONDARY ACCESSION(S): PRJNA239517

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Classifying leukemia types with chromatin conformation data

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-02-27 | E-GEOD-55408 | biostudies-arrayexpress

Classifying leukemia types with chromatin conformation data.

Project description:Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed.Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data.Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes.

| S-EPMC4038739 | biostudies-literature

Classifying leukemia types with chromatin conformation data (5C)

Project description:Background: Although genetic or epigenetic alterations have shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. Results: Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data. Conclusions: Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes. Analysis of 38 samples using 5C technology. All data normalized using a 'master' BAC consisting of 5C data from 6 samples.

2014-02-27 | E-GEOD-55406 | biostudies-arrayexpress

Classifying leukemia types with chromatin conformation data (ChIP-Seq)

Project description:Background: Although genetic or epigenetic alterations have shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. Results: Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data. Conclusions: Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes. Examination of CTCF and RAD21 binding sites in THP-1 cell.

2014-02-27 | E-GEOD-55407 | biostudies-arrayexpress

Classifying leukemia types with chromatin conformation data (5C)

2014-02-27 | GSE55406 | GEO

Classifying leukemia types with chromatin conformation data (ChIP-Seq)

2014-02-27 | GSE55407 | GEO

Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-08 | E-GEOD-71884 | biostudies-arrayexpress

Chromatin signature identifies monoallelic gene expression across mammalian cell types

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-06-17 | E-GEOD-67384 | biostudies-arrayexpress

Genome-wide chromatin maps of T-cell acute lymphoblastic leukemia (T-ALL)