Dataset Information

FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research.

ABSTRACT: Organ fibrosis represents a vital health threat that substantially contributes to yearly mortality rates. While a considerable amount of research has been conducted on fibrosis, these reports have only focused on specific organs as affected within distinct disorders. Accordingly, results from such studies have been unable to provide a comprehensive understanding of the pathological processes involved. Here, we describe the development of FibROAD, an open-access database that integrates evidence from fibrosis-associated disorders as obtained from both the literature and multi-omics data. This resource will greatly assist both researchers and clinicians in the comprehension and treatment of this condition. FibROAD currently involves an assembly of 232 strong evidence-based fibrosis-related genes (FRGs) as garnered from 909 PubMed publications and contains lists of multi-omics data from > 4000 samples including RNA-seq, single-cell RNA-seq, miRNA-seq, ChIP-seq, ATAC-seq MeDIP-seq and MBD-seq as obtained from 17 different organs in 5 species. Results from integrative analyses as obtained using FibROAD have demonstrated that FRGs can be indicators for a wide range of organ fibrosis and reveal potential pro-fibrotic candidate genes for fibrosis research. In conclusion, FibROAD serves as a convenient platform where researchers can acquire integrated evidence and a more comprehensive understanding of fibrosis-related disorders. Database URL https://www.fibroad.org.

SUBMITTER: Sun YZ

PROVIDER: S-EPMC9216539 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research.

Sun Yu-Zhe YZ Hu Yong-Fei YF Zhang Yan Y Wei Shu-Yi SY Yang Bei-Lei BL Xu Ying-Ping YP Rong Zhi-Li ZL Wang Dong D Yang Bin B

Database : the journal of biological databases and curation 20220301

Organ fibrosis represents a vital health threat that substantially contributes to yearly mortality rates. While a considerable amount of research has been conducted on fibrosis, these reports have only focused on specific organs as affected within distinct disorders. Accordingly, results from such studies have been unable to provide a comprehensive understanding of the pathological processes involved. Here, we describe the development of FibROAD, an open-access database that integrates evidence ...[more]

PMID: 35277958

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Project description:BackgroundThe use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs.ResultsThe process identified 13,054 candidate human, bovine, mouse or rat genes/proteins used to select potential porcine homologs by searching multiple online sources of porcine gene information. The data in the Porcine Translational Research Database (( http://www.ars.usda.gov/Services/docs.htm?docid=6065 ) is supported by >5800 references, and contains 65 data fields for each entry, including >9700 full length (5' and 3') unambiguous pig sequences, >2400 real time PCR assays and reactivity information on >1700 antibodies. It also contains gene and/or protein expression data for >2200 genes and identifies and corrects 8187 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) for 5337 porcine genes.ConclusionsThis database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. This database provides the first comprehensive description of three major Super-families or functionally related groups of proteins (Cluster of Differentiation (CD) Marker genes, Solute Carrier Superfamily, ATP binding Cassette Superfamily), and a comparative description of porcine microRNAs.

Dataset Information

FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research.

Publications

FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research.

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