▼ Public Database integrated in REDE
(1) Public database used for regulation data
1. UCSC: A comprehensive resource of genome assemblies and annotations. (Perez, et al., 2025).
2. NCBI: A large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. (Sayers, et al., 2025).
3. FAANG: A database for understanding the genotype to phenotype link in domesticated animals. (Harrison, et al., 2021).
4. AOD: An animal omics database to integrate available omics data for human and domestic animals. (Yu, et al., 2023).
5. RGD: A comprehensive repository of integrated genomics, transcriptomics, and epigenetics data of Ruminantia. (Fu, et al., 2022).
(2) Public database used for gene annotation
1. Ensembl: A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. (Harrison, et al., 2024).
2. UniProt: A comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. (UniProt Consortium, 2024).
3. Gene Ontology: A comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). (Gene Ontology Consortium, 2023).
(3) Public Data Used in DKthink-SII
1. SCREEN: A web interface for searching and visualizing the Registry of candidate cis-Regulatory Elements (cCREs) derived from ENCODE data. (ENCODE Project Consortium, 2020).
2. SilencerDB: A comprehensive database of silencers. (Zeng, et al., 2021).
3. UniProt: A comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. (UniProt Consortium, 2024).
4. Gene Ontology: A comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). (Gene Ontology Consortium, 2023).
5. Reactome: An core biological data resource that provides manually curated molecular details of a broad range of normal and disease-related biological processes. (Milacic, et al., 2024).
6. JASPAR: A widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for TFs across taxa. (Rauluseviciute, et al., 2024).
7. CIS-BP: A library of transcription factor (TF) DNA binding motifs and specificities. (Weirauch, et al., 2014).
8. TRRUST: A manually curated database of human and mouse transcriptional regulatory networks. (Han, et al., 2018).
9. ChEA3: A transcription factor enrichment analysis tool that ranks TFs associated with user-submitted gene sets. (Keenan, et al., 2019).
10. DoRothEA: A research resource that can be used to search candidate TF-drug interactions in cancer. (Garcia-Alonso, et al., 2018).