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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

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

ORGANISM(S): Homo sapiens

SUBMITTER: sujin Baek

PROVIDER: E-GEOD-46598 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer.

Project description:Abnormal DNA methylation is an epigenetic mechanism that promotes gastric carcinogenesis. While the abnormal methylation at promoter regions has been characterized for many genes, the function of DNA methylation marks at distal regulatory regions in gastric cancer remains poorly described. Here, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines to understand the epigenetic changes in the distal as well as the proximal regulatory regions. In total, 257,651 significant DMRs (Differentially methylated regions) were identified in gastric cancer, and the majority of these DMRs were located in the intergenic, intronic, and non-coding RNA regions. We identified the aberrant expression of many genes and lncRNAs due to changes in DNA methylation. Furthermore, we profiled the molecular subtype-specific methylation patterns in gastric cancer to characterize subtype-specific regulators that undergo DNA methylation changes. Our findings provide insights for understanding methylation changes at distal regulatory regions and reveal novel epigenetic targets in gastric cancer.

| S-EPMC5041931 | biostudies-literature

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines. mRNA sequencing profiles of normal tissue (n), purified gastric cancer (sc), and cultured gastric cancer cell (dc) were generated by deep sequencing, in five samples from three patients (csc1, csc2, csc3) and two replicates (csc1_sc2, csc1_sc3), using Illumina GAIIx and HiSeq2000.

2016-03-28 | E-GEOD-46597 | biostudies-arrayexpress

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines MBD sequencing of normal tissue (n), purified gastric cancer (sc), and cultured gastric cancer cell (dc) were generated by deep sequencing, in five samples from three patients (csc1, csc2, csc3) and two replicates (csc1_sc2, csc1_sc3), using Illumina GAIIx.

2016-03-28 | E-GEOD-46595 | biostudies-arrayexpress

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:We performed H3K27ac ChIP-seq data in seven gastric cancer cell lines to investigate the functional significance of epigenetic changes at distal regulatory regions H3K27ac ChIP-seq profiling of gastric cancer cell lines were generated by deep sequencing, in each seven samples, using Illumina GAIIx and Hiseq-2000

2016-03-28 | E-GEOD-75595 | biostudies-arrayexpress

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines.

2016-03-28 | GSE46597 | GEO

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines

2016-03-28 | GSE46595 | GEO

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-03-29 | GSE46598 | GEO

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:We performed H3K27ac ChIP-seq data in seven gastric cancer cell lines to investigate the functional significance of epigenetic changes at distal regulatory regions

2016-03-28 | GSE75595 | GEO

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

| PRJNA201422 | ENA

Predicting enhancer-promoter interaction based on epigenomic signals.

Project description:Introduction: The physical interactions between enhancers and promoters are often involved in gene transcriptional regulation. High tissue-specific enhancer-promoter interactions (EPIs) are responsible for the differential expression of genes. Experimental methods are time-consuming and labor-intensive in measuring EPIs. An alternative approach, machine learning, has been widely used to predict EPIs. However, most existing machine learning methods require a large number of functional genomic and epigenomic features as input, which limits the application to different cell lines. Methods: In this paper, we developed a random forest model, HARD (H3K27ac, ATAC-seq, RAD21, and Distance), to predict EPI using only four types of features. Results: Independent tests on a benchmark dataset showed that HARD outperforms other models with the fewest features. Discussion: Our results revealed that chromatin accessibility and the binding of cohesin are important for cell-line-specific EPIs. Furthermore, we trained the HARD model in the GM12878 cell line and performed testing in the HeLa cell line. The cross-cell-lines prediction also performs well, suggesting it has the potential to be applied to other cell lines.

| S-EPMC10151517 | biostudies-literature

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