title: AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource.
abstract: Transcriptome studies have shown the pervasive nature of transcription, demonstrating almost all the genes undergo alternative splicing. Accurately annotating all transcripts of a gene is crucial. It is needed to understand the impact of mutations on phenotypes, to shed light on genetic and epigenetic regulation of mRNAs and more generally to widen our knowledge about cell functionality and tissue diversity. RNA-sequencing (RNA-Seq), and the other applications of the next-generation sequencing, provides precious data to improve annotations' accuracy, simultaneously creating issues related to the variety, complexity and the size of produced data. In this 'scenario', the lack of user-friendly resources, easily accessible to researchers with low skills in bioinformatics, makes difficult to retrieve complete information about one or few genes without browsing a jungle of databases. Concordantly, the increasing amount of data from 'omics' technologies imposes to develop integrated databases merging different data formats coming from distinct but complementary sources. In light of these considerations, and given the wide interest in studying Down syndrome-a genetic condition due to the trisomy of human chromosome 21 (HSA21)-we developed an integrated relational database and a web interface, named ALE-HSA21 (AnaLysis of Expression on HSA21), accessible at http://bioinfo.na.iac.cnr.it/ALE-HSA21. This comprehensive and user-friendly web resource integrates-for all coding and noncoding transcripts of chromosome 21-existing gene annotations and transcripts identified de novo through RNA-Seq analysis with predictive computational analysis of regulatory sequences. Given the role of noncoding RNAs and untranslated regions of coding genes in key regulatory mechanisms, ALE-HSA21 is also an interesting web-based platform to investigate such processes. The 'transcript-centric' and easily-accessible nature of ALE-HSA21 makes this resource a valuable tool to rapidly retrieve data at the isoform level, rather than at gene level, useful to investigate any disease, molecular pathway or cell process involving chromosome 21 genes. Database URL: http://bioinfo.na.iac.cnr.it/ALE-HSA21/.
authors.affiliation: Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', National Research Council, Naples, Italy, Department of Pharmaceutical Sciences, University of Salerno, National Research Council, Fisciano, Salerno, Italy, Istituto per le Applicazioni del Calcolo 'Mauro Picone', National Research Council, Naples, Italy and Department of Biochemistry and Biophysics, Second University of Naples (SUN), Naples, Italy.
authors.forename: Margherita
authors.initials: M
authors.lastname: Scarpato
authors.forename: Roberta
authors.initials: R
authors.lastname: Esposito
authors.forename: Daniela
authors.initials: D
authors.lastname: Evangelista
authors.forename: Marianna
authors.initials: M
authors.lastname: Aprile
authors.forename: Maria Rosaria
authors.initials: MR
authors.lastname: Ambrosio
authors.forename: Claudia
authors.initials: C
authors.lastname: Angelini
authors.forename: Alfredo
authors.initials: A
authors.lastname: Ciccodicola
authors.forename: Valerio
authors.initials: V
authors.lastname: Costa
mesh_terms: D001483:Base Sequence; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics*; D003198:Computer Simulation; D003625:Data Collection; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D010865:Pilot Projects; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D022661:RNA, Untranslated