Human Ageing Genomic Resources
The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.[1]
HALL: a comprehensive database for human aging and longevity studies
Human Aging and Longevity Landscape (HALL), a comprehensive multi-omics repository encompassing a diverse spectrum of human cohorts, spanning from young adults to centenarians. The core objective of HALL is to foster healthy aging by offering an extensive repository of information on biomarkers that gauge the trajectory of human aging. Moreover, the database facilitates the development of diagnostic tools for aging-related conditions and empowers targeted interventions to enhance longevity. HALL is publicly available at https://ngdc.cncb.ac.cn/hall/index.[2]
Biolearn, an open-source library for biomarkers of aging
Identifying and validating biomarkers of aging is pivotal for understanding the aging process and testing longevity interventions. Biolearn is an open-source library (freely available at https://Bio-Learn.github.io/) dedicated to the implementation and application of aging biomarkers.[3]
Biolearn facilitates:
1. harmonization of existing aging biomarkers, while presenting a structured framework for novel biomarkers in standardized formats;
2. unification of public datasets, ensuring coherent structuring and formatting, thus simplifying cross-population validation studies; and
3. provision of computational methodologies to assess any harmonized biomarker against unified datasets.
A metabolic atlas of mouse aging
Cell Atlas of Worm Aging (CAWA)
Human Muscle Ageing Cell Atlas (HMA)
The Human Muscle Ageing Cell Atlas provides a series of integrated cellular and molecular explanations for sarcopenia and frailty development in advanced ages.[6][7]
Gene Expression Regulation Database (GREDB)
GereDB is an comprehensive cohort of gene expression regulation relationships curiated from published literatures. Geredb has been continually devepleted for more than 4 years, making it the one of the most trusted and complete collection of gene expression regulation database in the community.[8]
voyAGEr is an online graphical interface to explore age-related gene expression alterations in 49 human tissues.[9] voyAGEr was created to assist researchers with no expertise in bioinformatics, providing a supportive framework for elaborating, testing and refining their hypotheses on the molecular nature of human ageing and its association with pathologies, thereby also aiding in the discovery of novel therapeutic targets. voyAGEr is freely available at https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr. voyAGEr reveals transcriptomic signatures of the known asynchronous ageing between tissues, allowing the observation of tissue-specific age-periods of major transcriptional changes, associated with alterations in different biological pathways, cellular composition, and disease conditions.
GenAge
A major resource in HAGR is GenAge,[10] which includes a curated database of over 300 genes related to human ageing and a database of over 2,000 ageing- and longevity-associated genes in model organisms.
Functions for aging-related gene sets. All included genes are collected from aging-related literature and manually annotated. All gene sets are divided into ten sub-categories. The species currently listed include humans and mice.[11]
CodeKeeper™
CodeKeeper™ is BioViva's open access database for gene therapy. It is designed for anyone interested in what is happening in the gene therapy space. Advanced tools are available for universities, companies, independent researchers, and anyone else who is interested in understanding or contributing to the state-of-the-art.
Senescence promoting genes
Epigenomics
EWASdb : epigenome-wide association study database
Single-cell transcriptomics
Proteomics
GenAge Human Genes
This section of GenAge features genes possibly related to human ageing. Briefly, genes were selected for inclusion based on findings in model organisms put in context of human biology plus the few genes directly related to ageing in humans. As such, genes should be seen as candidate human ageing-associated genes.[14]
Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans
GenAge Model Organisms
Ageing and/or longevity in model organisms[15]
AnAge
Another major database in HAGR is AnAge.[16] Featuring over 4,000 species, AnAge provides a compilation of data on ageing, longevity, and life history that is ideal for the comparative biology of ageing.
DrugAge
DrugAge provides data on over 500 ageing-related drugs across model organisms.[17]
DrugCentral
DrugCentral, accessible at https://drugcentral.org , is an open-access online drug information repository. It covers over 4950 drugs, incorporating structural, physicochemical, and pharmacological details to support drug discovery, development, and repositioning.[18]
Pharmacogenomics
THE REJUVENATION ROADMAP
The cell rejuvenation atlas
SINGULAR (Single-cell RNA-seq Investigation of Rejuvenation Agents and Longevity), a cell rejuvenation atlas that provides a unified system biology analysis of diverse rejuvenation strategies across multiple organs at single-cell resolution.[19]
Code for the processing pipeline and auxiliary functions in the workflow is available at https://github.com/jarcoshodar/singularsource.
SINGULAR is available as a publicly available interactive database at https://singular.lcsb.uni.lu/. Source code for a local install and exploration of the data is available at https://git-r3lab.uni.lu/mohamed.soudy/singular.
References
- ↑ Human Ageing Genomic Resources
- ↑ Li, H., Wu, S., Li, J., Xiong, Z., Yang, K., Ye, W., ... & Zhang, W. (2023). HALL: a comprehensive database for human aging and longevity studies. Nucleic Acids Research, gkad880. DOI: 10.1093/nar/gkad880
- ↑ Ying, K., Paulson, S., Perez-Guevara, M., Emamifar, M., Casas Martinez, M., Kwon, D., ... & Gladyshev, V. N. (2023). Biolearn, an open-source library for biomarkers of aging. bioRxiv, 2023-12. https://doi.org/10.1101/2023.12.02.569722
- ↑ Steven E Pilley, et al., (2024). A metabolic atlas of mouse aging. bioRxiv; doi: https://doi.org/10.1101/2024.05.04.592445
- ↑ Gao, S.M., Qi, Y., Zhang, Q. et al. Aging atlas reveals cell-type-specific effects of pro-longevity strategies. Nat Aging (2024). https://doi.org/10.1038/s43587-024-00631-1
- ↑ Lai, Y., Ramírez-Pardo, I., Isern, J. et al. (2024). Multimodal cell atlas of the ageing human skeletal muscle. Nature https://doi.org/10.1038/s41586-024-07348-6
- ↑ Human Muscle Ageing Cell Atlas (HMA)
- ↑ Huang, T., Huang, X., Shi, B. & Yao, M. (2019). GEREDB: Gene expression regulation database curated by mining abstracts from literature. Journal of Bioinformatics and Computational Biology 17, 1950024 https://www.ncbi.nlm.nih.gov/pubmed/31617460
- ↑ Schneider A.L., Martins-Silva R., Kaizeler A., Saraiva-Agostinho N., Barbosa-Morais N. (2023). voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues. bioRxiv, 521681. doi: 10.1101/2022.12.22.521681; eLife 12:RP88623. https://doi.org/10.7554/eLife.88623.3
- ↑ GenAge Database of Ageing-Related Genes
- ↑ Aging-related gene sets
- ↑ Ma, S., Chi, X., Cai, Y., Ji, Z., Wang, S., Ren, J., & Liu, G. H. (2023). Decoding aging hallmarks at the single-cell level. Annual Review of Biomedical Data Science, 6. DOI: 10.1146/annurev-biodatasci-020722-120642
- ↑ Cai, Y., Xiong, M., Xin, Z., Liu, C., Ren, J., Yang, X., ... & Liu, G. H. (2023). Decoding aging-dependent regenerative decline across tissues at single-cell resolution. Cell Stem Cell. PMID: 37898124 DOI: 10.1016/j.stem.2023.09.014
- ↑ GenAge Human Genes
- ↑ GenAge Model Organisms
- ↑ AnAge Database of Animal Ageing and Longevity
- ↑ DrugAge Database of Anti-Ageing Drugs
- ↑ Halip, L., Avram, S., Curpan, R., Borota, A., Bora, A., Bologa, C., & Oprea, T. I. (2023). Exploring DrugCentral: from molecular structures to clinical effects. Journal of Computer-Aided Molecular Design, 1-14. PMID: 37707619 DOI: 10.1007/s10822-023-00529-x
- ↑ Hodar, J. A., Jung, S., Soudy, M., Barvaux, S., & Del Sol, A. (2024). The cell rejuvenation atlas: leveraging network biology to identify master regulators of rejuvenation strategies. Aging. 16(17), 12168—12190 PMID: 39264584 DOI: 10.18632/aging.206105
