Osteoarthritis Data Integration Portal (OsteoDIP): A web-based gene and non-coding RNA expression database.
Data integration
GEO, Gene Expression Omnibus
GWAS, Genome Wide Assocaition Studies
Gene expression
HGNC, HUGO Gene Nomenclature Committee
IID, Integrated Interactions Database
Long non-coding RNA
NAViGaTOR, NetworkAnalysis, Visualization, & Graphing TORonto
OA, osteoarthritis
OsteoDIP, Osteoarthritis Data Integration Portal
TCGA, The Cancer Genome Atlas
integrative computational biology
microRNA
mirDIP, MicroRNA Data Integration Portal
pathDIP, Pathway Data Integration Portal
Journal
Osteoarthritis and cartilage open
ISSN: 2665-9131
Titre abrégé: Osteoarthr Cartil Open
Pays: England
ID NLM: 101767068
Informations de publication
Date de publication:
Mar 2022
Mar 2022
Historique:
received:
01
03
2021
accepted:
19
01
2022
entrez:
7
12
2022
pubmed:
8
12
2022
medline:
8
12
2022
Statut:
epublish
Résumé
OsteoDIP aims to collect and provide, in a simple searchable format, curated high throughput RNA expression data related to osteoarthritis. Datasets are collected annually by searching "osteoarthritis gene expression profile" in PubMed. Only publications containing patient data and a list of differentially expressed genes are considered. From 2020, the search has expanded to include non-coding RNAs. Moreover, a search in GEO for "osteoarthritis" datasets has been performed using ' Out of 1204 curated papers, 63 have been included in OsteoDIP, while GEO curation led to the collection of 28 datasets. Literature data provides a snapshot of osteoarthritis research derived from 1924 human samples, while GEO datasets provide expression for additional 1012 patients. Similar to osteoarthritis literature, OsteoDIP data has been created mostly from studies focused on knee, and the tissue most frequently investigated is cartilage. GEO data sets were fully integrated with associated clinical data. We showcase examples and use cases applicable for translational research in osteoarthritis. OsteoDIP is publicly available at http://ophid.utoronto.ca/OsteoDIP. The website is easy to navigate and all the data is available for download. Data consolidation allows researchers to perform comparisons across studies and to combine data from different datasets. Our examples show how OsteoDIP can integrate with and improve osteoarthritis researchers' pipelines.
Identifiants
pubmed: 36474475
doi: 10.1016/j.ocarto.2022.100237
pii: S2665-9131(22)00005-X
pmc: PMC9718079
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100237Informations de copyright
© 2022 The Authors.
Déclaration de conflit d'intérêts
At the end of the text, under a subheading “Conflict of interest statement” all authors must disclose any financial and personal relationships with other people or organisations that could inappropriately influence (bias) their work. Examples of potential conflicts of interest include employment, consultancies, stock ownership, honoraria, paid expert testimony, patent applications/registrations, and research grants or other funding.
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