snoDB: An interconnected online database of human snoRNA

RNA is more than just a transitory molecule between DNA and proteins. Beyond the scope of protein-coding RNAs lies a vast underexplored landscape of non-coding RNAs (ncRNA). These RNAs have been slowly uncovered since the 1960s but it took until the turn of the century, and the advent of high-throughput RNA-Sequencing methodologies, for us to finally see how dominated by ncRNAs the transcriptome really is. High-throughput experiments also exponentially expanded the amount of data on RNA and created a need for bioinformatics tools for their analysis and storage. One of the first, and most abundant, ncRNA types to be discovered was small nucleolar RNAs (snoRNAs). Canonically pegged as guides for the modification of pre-ribosomal RNAs, these highly conserved RNAs now boast a diverse list of crucial non-canonical roles, notably in gene expression, as well as being associated to a myriad of diseases and cancers. Considering the growing body of literature surrounding snoRNAs in humans, and their increasing connections to a broad range of fields of study, having an accessible and comprehensive assessment of these data has become essential. Unfortunately, existing online human snoRNA databases, snoRNABase, snOPY, and snoRNA Atlas, are either outdated or too narrow in scope, focusing almost exclusively on canonical snoRNA interactions and lacking expression data. As such, we have created snoDB: a modern, interactive database of human snoRNAs with curated data on non-canonical snoRNA interactions, expression data in a growing range of tissues and cell lines, and more. Unlike the old snoRNA databases, snoDB features extensive visualisation and filtering capabilities, allowing for its larger array of data to be selectively viewed in an interactive and customizable table. Expression data can be further visualised in interactive heatmaps thanks to snoDB’s sister tool: snoTHAW. snoDB also innovates by being much more interconnected with other resources. Data was gathered, and joined together in a relational postgreSQL database, from over a dozen resources, including the RNAcentral database consortium, the largest database of ncRNA sequences, of which snoDB is now a part of. In addition, all resources are linked to in-table, where data they provided appears, to help corroborate the data shown for transparency, as well as to grant access to interesting features housed on remote sites. Finally, snoDB is built to be easily maintainable, updatable and extensible to keep up with ongoing developments and insure that the information it contains will contribute to snoRNA research for years to come.

Name thesis:degree_name

M. Sc.

Level thesis:degree_level

Maîtrise

Discipline thesis:degree_discipline

Biochimie

Grantor dc:publisher

Université de Sherbrooke

Year dc:date.issued

2020

Author dc:creator

• Bouchard-Bourelle, Philia

Advisors dc:contributor.advisor

• Abou Elela, Sherif
• Scott, Michelle

• Petits ARN nucléolaire
• Bio-informatique
• Base de données (PostgreSQL)
• Séquençage d’ARN
• Intéractions ARN-ARN
• Datatables
• snoRNA
• Bioinformatics
• RNA-Seq
• Database
• PostgreSQL (PSQL)
• RNA-RNA Interactions

Licence dc:rights.uri

• http://creativecommons.org/licenses/by-nc-sa/2.5/ca/

Language dc:language.iso

en

Handle dc:identifier.uri

http://hdl.handle.net/11143/16402

OAI identifier oai:identifier

oai:usherbrooke.scholaris.ca:11143/16402