ArticleBMC genomics2020
intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Transgenerational effects of heat shock on gene regulation and fitness-related traits in natural Drosophila populations.Molecular biology and evolution · 2026Article
- Integrative multiomics reveals common endotypes across PSEN1, PSEN2, and APP mutations in familial Alzheimer's disease.Alzheimer's research & therapy · 2025Article
- A holistic approach to understanding immune-mediated inflammatory diseases: bioinformatic tools to integrate omics data.Computational and structural biotechnology journal · 2024Review
- Epithelial cells maintain memory of prior infection with Streptococcus pneumoniae through di-methylation of histone H3.Nature communications · 2024Article
- epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation.Briefings in bioinformatics · 2024Article
- SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development.Nature communications · 2023Article
- Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation.Genome biology · 2023Article
- Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods.Computational and structural biotechnology journal · 2023Review
- Vitamin D and Systems Biology.Nutrients · 2022Review
- Transcriptomic and ChIP-seq Integrative Analysis Identifies KDM5A-Target Genes in Cardiac Fibroblasts.Frontiers in cardiovascular medicine · 2022Article
- The International Conference on Intelligent Biology and Medicine (ICIBM) 2020: Scalable techniques and algorithms for computational genomics.BMC genomics · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundRNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions. Gene expression is regulated by several mechanisms, including epigenetically by post-translational histone modifications which can be assessed by ChIP-Seq (Chromatin Immuno-Precipitation Sequencing). As more and more biological samples are analyzed by the combination of ChIP-Seq and RNA-Seq, the integrated analysis of the corresponding data sets becomes, theoretically, a unique option to study gene regulation. However, technically such analyses are still in their infancy.
resultsHere we introduce intePareto, a computational tool for the integrative analysis of RNA-Seq and ChIP-Seq data. With intePareto we match RNA-Seq and ChIP-Seq data at the level of genes, perform differential expression analysis between biological conditions, and prioritize genes with consistent changes in RNA-Seq and ChIP-Seq data using Pareto optimization.
conclusionintePareto facilitates comprehensive understanding of high dimensional transcriptomic and epigenomic data. Its superiority to a naive differential gene expression analysis with RNA-Seq and available integrative approach is demonstrated by analyzing a public dataset.
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