GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

Abstract

We release GeneBase 1.1, a local tool with a graphical interface useful for parsing, structuring and indexing data from the National Center for Biotechnology Information (NCBI) Gene data bank. Compared to its predecessor GeneBase (1.0), GeneBase 1.1 now allows dynamic calculation and summarization in terms of median, mean, standard deviation and total for many quantitative parameters associated with genes, gene transcripts and gene features (exons, introns, coding sequences, untranslated regions). GeneBase 1.1 thus offers the opportunity to perform analyses of the main gene structure parameters also following the search for any set of genes with the desired characteristics, allowing unique functionalities not provided by the NCBI Gene itself. In order to show the potential of our tool for local parsing, structuring and dynamic summarizing of publicly available databases for data retrieval, analysis and testing of biological hypotheses, we provide as a sample application a revised set of statistics for human nuclear genes, gene transcripts and gene features. In contrast with previous estimations strongly underestimating the length of human genes, a 'mean' human protein-coding gene is 67 kbp long, has eleven 309 bp long exons and ten 6355 bp long introns. Median, mean and extreme values are provided for many other features offering an updated reference source for human genome studies, data useful to set parameters for bioinformatic tools and interesting clues to the biomedical meaning of the gene features themselves.Database URL: http://apollo11.isto.unibo.it/software/.

Figure 1.

(A) Gene type composition of GeneBase 1.1 Human entries for a total of 59 801 genes and (B) for 22 451 ‘REVIEWED’ or ‘VALIDATED’ genes with at least one ‘REVIEWED’ or ‘VALIDATED’ transcript (genes not in current annotation release are excluded). Gene type labels are derived from ‘Gene_Type’ field of GeneBase 1.1 Human ‘Gene_Summary’ table as annotated in NCBI Gene as follows: protein-coding, pseudo (pseudogenes), ncRNA (non-coding RNA), snoRNA (small nucleolar RNA), snRNA (small nuclear RNA), rRNA (ribosomal RNA), tRNA (transfer RNA), ‘other’ and ‘unknown’.

Figure 2.

Number of ‘REVIEWED’ or ‘VALIDATED’ genes with at least one ‘REVIEWED’ or ‘VALIDATED’ transcript in GeneBase 1.1 Human (genes not in current annotation release are excluded) divided in protein-coding genes, pseudogenes and non-coding genes (which include genes for ribosomal RNAs, small nucleolar RNAs, small nuclear RNAs and non-coding RNAs) for each human chromosome. See Table 1 and Supplementary Table S2 for more details.

Figure 3.

Exon (A) and intron (B) length distributions considering GeneBase 1.1 Human ‘Gene_Table’ records with a ‘VALIDATED’ or ‘REVIEWED’ RefSeq status, with an ‘NM_’ (protein-coding RNAs, continuous lines) or ‘NR_’ (non-coding RNAs, dotted lines) type of corresponding RefSeq RNA accession number, belonging to ‘REVIEWED’ or ‘VALIDATED’ genes excluding those not in current annotation release.