A well-known limit of genome browsers is that the large amount of genome and gene data is not organized in the form of a searchable database, hampering full management of numerical data and free calculations. Due to the continuous increase of data deposited in genomic repositories, their content revision and analysis is recommended. Using GeneBase, a software with a graphical interface able to import and elaborate National Center for Biotechnology Information (NCBI) Gene database entries, we provide tabulated spreadsheets updated to 2019 about human nuclear protein-coding gene data set ready to be used for any type of analysis about genes, transcripts and gene organization.
Comparison with previous reports reveals substantial change in the number of known nuclear protein-coding genes (now 19,116), the protein-coding non-redundant transcriptome space [now 59,281,518 base pair (bp), 10.1% increase], the number of exons (now 562,164, 36.2% increase) due to a relevant increase of the RNA isoforms recorded. Other parameters such as gene, exon or intron mean and extreme length appear to have reached a stability that is unlikely to be substantially modified by human genome data updates, at least regarding protein-coding genes. Finally, we confirm that there are no human introns shorter than 30 bp.
A well-known limit of genome browsers [1,2,3] is that the large amount of data they provide about human genome and genes is not organized in the form of a searchable database , hampering a full management of numerical data and free calculations on data subsets. We have previously shown that GeneBase, a software with a graphical interface able to import and elaborate data available in the National Center for Biotechnology Information (NCBI) Gene database, allows users to perform original searches, calculations and analyses of the main gene-associated meta-information , and since the release of GeneBase 1.1, it can also provide descriptive statistical summarization such as median, mean, standard deviation and total for many quantitative parameters associated with genes, gene transcripts and gene features for any desired database subset .
Due to the continuous increase of data deposited in genomic repositories, a revision and analysis of their content is recommended. We provide here a tabulated set of data about human nuclear protein-coding genes that may be useful for human genome studies and analysis. While the basic approach to obtain the data we present here is similar to the one followed in our previous study about the subject , there are two main differences. First, the data are now updated as of January 2019 rather than January 2016, exploiting novel information made available in the last 3 years and thus showing how some parameters have been subjected to relevant changes, while others appear to be stable.
In addition, following analysis based on the relationships between different data tables provided by the database at the core of the GeneBase tool, we provide the results in the simple form of a spreadsheet table, providing three data sets ready to be used for any type of analysis of the data about nuclear protein-coding genes, transcripts and gene organization (exons, coding exons and introns). In order to provide reliable data, we focused on a curated subset of human nuclear protein-coding genes with a REVIEWED or VALIDATED Reference Sequence (RefSeq) status [1, 7]. The reasons for the choice of the NCBI Gene database as a reference data source have been previously discussed in detail .
Main summarized data derived from the analysis of our updated and standard-formatted data sets are also provided here, while the data tables remain available for human genome studies.