{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Zhao Y"],"funding":["National Cancer Institute","NCI NIH HHS","National Institutes of Health"],"pagination":["269"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8220791"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["19(1)"],"pubmed_abstract":["Background
In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as differential gene expression between two or more conditions. Several methods have been proposed and continue to be used. However, a consensus has not been reached regarding the best gene expression quantification method for RNA-seq data analysis.Methods
In the present study, we used replicate samples from each of 20 patient-derived xenograft (PDX) models spanning 15 tumor types, for a total of 61 human tumor xenograft samples available through the NCI patient-derived model repository (PDMR). We compared the reproducibility across replicate sampl"],"journal":["Journal of translational medicine"],"pubmed_title":["TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository."],"pmcid":["PMC8220791"],"funding_grant_id":["HHSN261200800001E"],"pubmed_authors":["Williams PM","Doroshow JH","Das B","Li MC","Chen L","Karlovich C","Konate MM","Evrard YA","Zhao Y","McShane LM"],"additional_accession":[]},"is_claimable":false,"name":"TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository.","description":"Background
In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as differential gene expression between two or more conditions. Several methods have been proposed and continue to be used. However, a consensus has not been reached regarding the best gene expression quantification method for RNA-seq data analysis.Methods
In the present study, we used replicate samples from each of 20 patient-derived xenograft (PDX) models spanning 15 tumor types, for a total of 61 human tumor xenograft samples available through the NCI patient-derived model repository (PDMR). We compared the reproducibility across replicate sampl","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Jun","modification":"2026-05-08T00:29:09.864Z","creation":"2022-02-10T15:58:31.158Z"},"accession":"S-EPMC8220791","cross_references":{"pubmed":["34158060"],"doi":["10.1186/s12967-021-02936-w"]}}