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AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource

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 epigenet...

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Autores principales: Scarpato, Margherita, Esposito, Roberta, Evangelista, Daniela, Aprile, Marianna, Ambrosio, Maria Rosaria, Angelini, Claudia, Ciccodicola, Alfredo, Costa, Valerio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3935309/
https://www.ncbi.nlm.nih.gov/pubmed/24573881
http://dx.doi.org/10.1093/database/bau009
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author Scarpato, Margherita
Esposito, Roberta
Evangelista, Daniela
Aprile, Marianna
Ambrosio, Maria Rosaria
Angelini, Claudia
Ciccodicola, Alfredo
Costa, Valerio
author_facet Scarpato, Margherita
Esposito, Roberta
Evangelista, Daniela
Aprile, Marianna
Ambrosio, Maria Rosaria
Angelini, Claudia
Ciccodicola, Alfredo
Costa, Valerio
author_sort Scarpato, Margherita
collection PubMed
description 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/
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spelling pubmed-39353092014-02-26 AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource Scarpato, Margherita Esposito, Roberta Evangelista, Daniela Aprile, Marianna Ambrosio, Maria Rosaria Angelini, Claudia Ciccodicola, Alfredo Costa, Valerio Database (Oxford) Original Article 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/ Oxford University Press 2014-02-25 /pmc/articles/PMC3935309/ /pubmed/24573881 http://dx.doi.org/10.1093/database/bau009 Text en © The Author(s) 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Scarpato, Margherita
Esposito, Roberta
Evangelista, Daniela
Aprile, Marianna
Ambrosio, Maria Rosaria
Angelini, Claudia
Ciccodicola, Alfredo
Costa, Valerio
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource
title AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource
title_full AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource
title_fullStr AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource
title_full_unstemmed AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource
title_short AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource
title_sort analysis of expression on human chromosome 21, ale-hsa21: a pilot integrated web resource
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3935309/
https://www.ncbi.nlm.nih.gov/pubmed/24573881
http://dx.doi.org/10.1093/database/bau009
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