Table 13 Data sources used in Naïve Bayes classifier for candidate aging genes

Literature

OBO

AgeFactDB

The ageing-related information included both by manual and automatic information extraction from the scientific literature.

https://lov.linkeddata.es/dataset/lov/vocabs/obo

http://agefactdb.jenage.de/

Functional annotation

David

The list of all functional annotation.

https://david.ncifcrf.gov/

Biological pathways

Reactome

Kegg

The list of biological pathway.

https://reactome.org/

https://www.genome.jp/kegg/pathway.html

Gene Ontology

GO

The Biological Process, Molecular Function, and Cellular Component vocabularies.

http://www.geneontology.org/

Phenotype

HPO

OMIM

The list of all ageing-related phenotype and associated gene.

https://hpo.jax.org/

https://www.omim.org/

Intrinsic properties

Pfam

PDB

The chromosome number, location, gene segment, gene type, etc.

https://pfam.xfam.org/

https://www.rcsb.org/

Sequence

RefSeq

The list of all known active site, binding site, chain, etc.

https://www.ncbi.nlm.nih.gov/refseq/

Protein-Protein Interaction

HPRD

String

The list of each gene had a physical interaction with each of the positive genes.

http://www.hprd.org/

https://string-db.org/

Gene expression

GEO

HAGR

The ageing-related expression included tissue type, overexpressed and under expressed, etc.

https://www.ncbi.nlm.nih.gov/geo/

http://genomics.senescence.info/gene_expression/index.php

Regulatory

RegNetwork

The list of all regulatory relationship, such as miRNA, Transcription factor, etc.

http://www.regnetworkweb.org/

Orthologues

CDD

HomoloGene

OrthoDB

The catalog of orthologous protein-coding genes across vertebrates and known conserved domain.

https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

https://www.ncbi.nlm.nih.gov/homologene

https://www.orthodb.org/