Gene name errors: Lessons not learned

Abstract

Erroneous conversion of gene names into other dates and other data types has been a frustration for computational biologists for years. We hypothesized that such errors in supplementary files might diminish after a report in 2016 highlighting the extent of the problem. To assess this, we performed a scan of supplementary files published in PubMed Central from 2014 to 2020. Overall, gene name errors continued to accumulate unabated in the period after 2016. An improved scanning software we developed identified gene name errors in 30.9% (3,436/11,117) of articles with supplementary Excel gene lists; a figure significantly higher than previously estimated. This is due to gene names being converted not just to dates and floating-point numbers, but also to internal date format (five-digit numbers). These findings further reinforce that spreadsheets are ill-suited to use with large genomic data.

Fig 1. Prevalence of gene name errors in the period 2014–2020.

(A) Publications with supplementary Excel gene lists. (B) Publications affected by gene name errors. (C) Proportion of affected publications.

Fig 2. A scatterplot of JIF and proportion of articles with supplementary Excel gene lists affected by gene name errors.

Fig 3. Gene name errors in supplementary files for three dominant journals in the period 2014–2020.