![]() Dev signature contains genes with large variation in expression across samples. Pearson signature represents the genes highly correlated with chronological age by Pearson correlation. DESeq2 signature was obtained by performing differential expression analysis on each tissue and select the top differential expressed genes. ![]() In the case that this argument is provided, it should be one of the following signatures. Otherwise, the across tissue signature “GTExAge” will be used. In the case that this argument is not provided, if tissue argument is also provided and the tissue is in the list above, the tissue specific age signature given by our DESeq2 analysis result on GTEx data will be used. Signature is a string which indicate the age signature to use when calculating RNA age. A detailed explanation can be found in our paper. (De Magalhães, Curado, and Church 2009) to find the genes with the largest number of age-related signals. To identify genes consistently differentially expressed across tissues, we adapted the binomial test discussed in de Magalhaes et al. The across-tissue calculator was constructed by first performing differential expression analysis on the RNASeq count data for each individual tissue. Chronological age was response variable whereas logarithm transformed FPKM of genes were predictors. FPKM values were calculated for each individual sample using getRPKM function in Bioconductor package recount.įor the tissue-specific RNASeq age calculator, elastic net (Zou and Hastie 2005) algorithm was used to train the predictors for each individual tissue. 2017) version of GTEx data, where all samples were processed with the same analytical pipeline. To facilitate integrated analysis and direct comparison of multiple datasets, we utilized recount2 (Collado-Torres et al. To avoid the influence of tumor on gene expression, the 102 tumor samples from GTEx V6 release are dropped and the remaining 9,560 samples were used in the subsequent analysis. GTEx V6 release contains gene expression data at gene, exon, and transcript level of 9,662 samples from 30 different tissues. GTEx is a public available genetic database for studying tissue specific gene expression and regulation. We utilized the GTEx data to construct our across-tissue and tissue-specific transcriptional age calculator.
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