Additional file 1 of 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
Creators: name: Zhao, Yingdong
name: Li, Ming-Chung
name: Konaté, Mariam M.
name: Chen, Li
name: Das, Biswajit
name: Karlovich, Chris
name: Williams, P. Mickey
name: Evrard, Yvonne A.
name: Doroshow, James H.
name: McShane, Lisa M.
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Details of the patient-derived xenograft samples used in this study (downloaded on Sept. 16, 2020 from the NCI PDMR database). Table S2. Summary statistics for CV values including interquartile range for different quantitative measures. Table S3A. Percentage of transcripts representing each of the top five most abundant genes in four PDX models whose TPM data had the highest median CV values. Table S3B. Percentage of transcripts representing each of the top five most abundant genes in five PDX models whose TPM data had the lowest median CV values. Figure S1. (A) Hierarchical clustering of 61 PDX samples using TMM normalized gene-level count data. (B) Hierarchical clustering of 61 PDX samples using FPKM data. (C) Hierarchical clustering of 61 PDX samples using Z-score on TPM-level data. Distance metric 1-Pearson correlation was used to generate the dendrogram in each right panel and Euclidean distance was used for the dendrogram in each left panel. Discordant models are highlighted with different color labels. Figure S2. Maximum distance (1-Pearson correlation) between replicate samples for the four PDX models with high median CV values using different gene expression quantification measures. Figure S3. (A) Hierarchical clustering of 61 PDX samples using TMM normalized TPM data. Distance metric 1-Pearson correlation was used to generate the dendrogram in the right panel and Euclidean distance was used for the dendrogram in the left panel. (B) Pairwise scatter plots comparing normalized TPM values for all genes among replicates of PDX model 475296-252-R. The x- and y- axes are normalized log2 counts on all pairwise scatter plots. Plots along the diagonal represent the density of the respective variable. Figure S4. Bar plot of median CVs for gene expression levels from replicate samples of each PDX model using different quantification measures. Figure S5. (A) Pairwise scatter plots comparing TPM values for all genes between replicate samples of PDX model 695221-133-T. (B) Pairwise scatter plots comparing DESeq2 normalized count values for all genes between replicate samples of PDX model 695221-133-T. The x- and y-axes are normalized log2 counts on all pairwise scatter plots. Plots along the diagonal represent the density of the respective variable. Figure S6. (A) Pairwise scatter plots comparing TPM values for all genes between replicate samples of PDX model 821394-179-R. (B) Pairwise scatter plots comparing DESeq2 normalized count values for all genes between replicate samples of PDX model 821394-179-R. The x- and y-axes are normalized log2 counts on all pairwise scatter plots. Plots along the diagonal represent the density of the respective variable. Figure S7. (A) Pairwise scatter plots comparing TPM values for all genes between replicate samples of PDX model K98449-230-R. (B) Pairwise scatter plots comparing DESeq2 normalized count values for all genes between replicate samples of PDX model K98449-230-R. The x- and y-axes are normalized log2 counts on all pairwise scatter plots. Plots along the diagonal represent the density of the respective variable. Figure S8. (A) Pairwise scatter plots comparing TPM values for all genes between replicate samples of PDX model 983718-287-R. (B) Pairwise scatter plots comparing TPM values for all genes between replicate samples of PDX model 884782-307-R. The x- and y-axes are normalized log2 counts on all pairwise scatter plots. Plots along the diagonal represent the density of the respective variable.