Gene-level differential analysis at transcript-level resolution

Gene-level differential analysis at transcript-level resolution

Gene-level differential expression analysis based on RNA-Seq is more robust, powerful and biologically actionable than transcript-level differential analysis. However aggregation of transcript counts prior to analysis results can mask transcript-level dynamics. We demonstrate that aggregating the results of transcript-level analysis allow for gene-level analysis with transcript-level resolution...

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome of cells. Many transcriptomic studies aim at comparing either abundance levels or the transcriptome composition between given conditions, and as a first step, the sequencing reads must be used as the basis for abundance quantification of transcriptomic features of interest, such as genes or transc...

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences Supplementary Material

The sim2 data set consists of simulated sequencing reads from the human chromosome 1. The sequencing parameters as well as underlying TPM values for the 15,677 transcripts in one of the two simulated conditions were estimated using RSEM v1.2.21 [6] from the ERS326990 sample from the ArrayExpress data set with accession number E MTAB 1733. We simulated three biological replicates from each of tw...

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences [version 2; referees: 2 approved]

High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome of cells. Many transcriptomic studies aim at comparing either abundance levels or the transcriptome composition between given conditions, and as a first step, the sequencing reads must be used as the basis for abundance quantification of transcriptomic features of interest, such as genes or transc...

rapid quantitative determination of gstp1 promoter methylation level using differential high resolution melting analysis (d-hrma)