ArticleDatabase : the journal of biological databases and curation2016
GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
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- Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples.American journal of human genetics · 2025Article
- Massively parallel reporter assays identify functional enhancer variants at QT interval GWAS loci.bioRxiv : the preprint server for biology · 2025Article
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- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
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- Chemical Modifications in Nucleic Acid Therapeutics.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Exploring autism spectrum disorder and co-occurring trait associations to elucidate multivariate genetic mechanisms and insights.BMC psychiatry · 2024Article
- Exploration of compatibility rules and discovery of active ingredients in TCM formulas by network pharmacology.Chinese herbal medicines · 2024Review
- Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples.bioRxiv : the preprint server for biology · 2024Article
- Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.Cell · 2024Article
- Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci.Nature communications · 2024Article
- Genomic language model predicts protein co-regulation and function.Nature communications · 2024Article
- Cost and time-efficient construction of a 3'-end mRNA library from unpurified bulk RNA in a single tube.Experimental & molecular medicine · 2024Article
- An optimized workflow of full-length transcriptome sequencing for accurate fusion transcript identification.RNA biology · 2024Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
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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/.
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