{"doi":"10.1186/s13040-024-00374-0","title":"Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation","abstract":"BACKGROUND: Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from the transcriptome versus the methylome (DNAm) influence estimates of differentially expressed genes (DEGs) and differentially methylated positions (DMPs). METHODS: Transcriptome and DNAm data were obtained from PBMC RNA and DNA of Kenyan children (n = 8) before, during, and 6 weeks following uncomplicated malaria. DEGs and DMPs between time points were detected using cell-type adjusted modeling with Cibersortx or IDOL, respectively. RESULTS: Most major cell types and principal components had moderate to high correlation between the two deconvolution methods (r = 0.60-0.96). Estimates of cell-type proportions and DEGs or DMPs were largely unaffected by the method, with the greatest discrepancy in the estimation of neutrophils. CONCLUSION: Variation in cell-type proportions is captured similarly by both transcriptomic and methylome deconvolution methods for most major cell types.","journal":"BioData Mining","year":2024,"id":450385,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9469,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":328176,"name":"Carmen J. Marsit","orcid":"0000-0003-4566-150X","position":1,"is_corresponding":false},{"id":548432,"name":"Arlene E. Dent","orcid":"0000-0003-2265-7938","position":2,"is_corresponding":false},{"id":951749,"name":"Paula Embury","orcid":null,"position":3,"is_corresponding":false},{"id":504574,"name":"Sidney Ogolla","orcid":"0000-0003-1570-6164","position":4,"is_corresponding":false},{"id":951750,"name":"David Midem","orcid":null,"position":5,"is_corresponding":false},{"id":48175,"name":"SCOTT M. WILLIAMS","orcid":"0000-0002-4835-9544","position":6,"is_corresponding":false},{"id":339359,"name":"James W. Kazura","orcid":"0000-0002-6390-634X","position":7,"is_corresponding":false},{"id":1270510,"name":"Emily R Hannon","orcid":"0000-0003-1905-7544","position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":null,"created_at":"2026-07-19T02:02:25.004119Z","pmid":"38992677","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}