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Fig. 1 | Genome Biology

Fig. 1

From: Gene-level differential analysis at transcript-level resolution

Fig. 1

Conversion of transcript counts to gene counts for the Nkap gene in the dexamethasone dataset under two conditions (dexamethasone and vehicle treatment). The x-axis is labeled with the Ensembl gene and transcript IDs, along with p values obtained by performing sleuth on transcripts and genes. In this process, the transcript counts (a) are converted into transcript abundances (b) by normalization according to transcript lengths. Transcript abundances are then summed to obtain gene abundances (c) and then converted to gene counts (d) using the median or mean transcript length as a proxy for the gene length. The converted gene counts mask significant changes among the constituent transcripts and the gene count variance does not directly reflect the combined variance in transcript counts. In this example, Nkap is not differential when examined using the converted gene counts, but can be identified as differential when the p values of the constituent transcripts are aggregated using the Lancaster method

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