Resources

A non-comprehensive list of websites and data resources relevant to research on healthy aging and longevity.

Human Aging

  1. Digital Aging Atlas

http://ageing-map.org/

Catalog of age-related changes in molecular markers, gene expression, pathology, physiology, and psychology.

  1. Human Aging Genomic Resources

http://genomics.senescence.info/

Includes the following databases:

  • GenAge – curated database of genes related to human aging
  • GenDR – genes associated with dietary restriction
  • AnAge – comparative biology of aging
  • LongevityMap – database of human genetic variants associated with longevity
  1. Human Mortality Database

http://www.mortality.org/

Mortality and population data for 37 countries or areas.

  1. GWAS Resource for Age-related Traits

https://ifar-great.hsl.harvard.edu/

Collection of musculoskeletal GWAS results.

  1. NIA Population Studies Database

http://nihlibrary.ors.nih.gov/nia/ps/niadb.asp

  1. NIA aging cell repository

http://ccr.coriell.org/Sections/Collections/NIA/?SsId=9

Drug discovery/small molecules

  1. NIH Chemical Genomics Center

http://www.ncats.nih.gov/research/reengineering/ncgc/ncgc.html

  1. High-Throughput Drug Screening Facility (at Memorial Sloan- Kettering)

http://www.mskcc.org/research/high-throughput-drug-screening-facility (drug screening)

  3.   NIH Pharmacogenomics Research Network

http://www.nigms.nih.gov/Research/FeaturedPrograms/PGRN/

  1. Extramural Pharmacogenomics Research Network (PGRN)

http://www.pgrn.org/display/pgrnwebsite/PGRN+Home

  1. PharmGKB

http://www.pharmgkb.org/

PharmGKB is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for researchers and clinicians.

  1. DTP Data

http://dtp.nci.nih.gov/index.html

Developmental Therapeutics Program at NCI/NIH.

  1. Molecular Library Centers (MLP)

http://mli.nih.gov/mli/

NIH initiative designed to discover small molecules that interact with biologically important proteins and pathways and to provide open access to the bioassay and chemical data generated by its research centers.

  1. ChemSpider

http://www.chemspider.com/

Chemical structure database.

  1. ChEMBL

https://www.ebi.ac.uk/chembldb/

ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). Includes molecular targets of small molecules where data is available.

  1. OpenEye cheminformatics software

http://www.eyesopen.com/

Software to facilitate the identification of small molecules that target known proteins. Free academic licenses are available under some circumstances; contact them for more details.

  1. PubChem

http://pubchem.ncbi.nlm.nih.gov/

Database of small molecule properties and targets.

  1. Drugbank

http://www.drugbank.ca/

The DrugBank database combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

  1. SuperTarget

http://bioinf-apache.charite.de/supertarget_v2/

Database of drug-target interactions.

  1. BindingDB

http://www.bindingdb.org/bind/index.jsp

BindingDB is a database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.

  1. STITCH

http://stitch.embl.de/

STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

  1. Mining the Druggable genome

http://dgidb.genome.wustl.edu/

Search for drug-gene interactions.

  1. NIA Interventions Testing Program

http://www.nia.nih.gov/research/dab/interventions-testing-program-itp

NIA’s ITP is a multi-institutional study investigating treatments with the potential to extend lifespan and delay disease and dysfunction in mice.

 

Human Genetic variation and annotation

  1. Wellcome Trust Sanger Institute

http://www.sanger.ac.uk/resources/databases/ genomics and related information

2.  Genevar (GENe Expression VARiation)

http://www.sanger.ac.uk/resources/software/genevar/

Genevar is a platform of database and web services designed for integrative analysis and visualization of SNP-gene associations in eQTL (expression quantitative trait loci) studies.

  1. HapMap

http://hapmap.ncbi.nlm.nih.gov/

Population genetic variation.

  1. 1000 Genomes project

http://www.1000genomes.org/

Population genetic variation from next-gen sequencing of more than 1000 individuals from about 25 populations.

  1. Variant Annotation Tool

http://vat.gersteinlab.org/index.php

Used by the 1000 genomes project.

  1. ANNOVAR

http://www.openbioinformatics.org/annovar/

Perl scripts to annotate genetic variants.

  1. UCSC genome browser

http://genome.ucsc.edu/

Genomic annotation for many genomes across taxa. Data is downloadable.

  1. Geuvadis Data browser.

http://www.ebi.ac.uk/Tools/geuvadis-das/

Displays eQTL results from approximately 100 samples from the 1000 genomes project. RNA levels measured using RNA-Seq, and genetic variation from 1000 genomes, resulting in a deep eQTL catalog.

  1. ScanDB

http://www.scandb.org/newinterface/about.html

Functional annotation of genetic variants. Houses eQTL results from a number of studies.

  1. ENCODE

http://www.genome.gov/10005107

https://genome.ucsc.edu/ENCODE/

  1. GWAS catalog

http://www.genome.gov/26525384

  1. Roadmap Epigenomics

http://www.roadmapepigenomics.org/

  1. RegulomeDB

http://www.regulomedb.org/

Functional annotation of genetic variation incorporating ENCODE data

  1. HaploReg

http://www.broadinstitute.org/mammals/haploreg/haploreg.php

Functional annotation of genetic variation incorporating ENCODE data, roadmap epigenome data, and eQTLs from GTex browser.

  1. Genotype-Tissue Expression (GTex)

commonfund.nih.gov/GTEx/index

http://www.broadinstitute.org/gtex/

eQTL browser can be found here:

http://www.ncbi.nlm.nih.gov/gtex/GTEX2/gtex.cgi

  1. Database of genotypes and phenotypes (dbGaP)

            http://www.ncbi.nlm.nih.gov/gap

  1. CHARGE consortium

            http://depts.washington.edu/chargeco/wiki/Main_Page

Consortium of cohorts with genome-wide genetic data and age-related phenotypes.

  1. Michigan Center for Statistical Genetics

http://csg.sph.umich.edu/

Useful data and software for genetic epidemiology

  1. TargetScan

http://www.targetscan.org/

Prediction of miRNA targets

  1. eQTL resources at the Pritchard Lab

http://eqtl.uchicago.edu/

  1. Variant annotation software SnpEff

http://snpeff.sourceforge.net/

  1. Variant annotation software SG-Adviser

http://genomics.scripps.edu/ADVISER/

 

General genomics and molecular biology

  1. NIH National Center for Biotechnology Information (NCBI)

http://www.ncbi.nlm.nih.gov/

  1. UniProt

http://www.uniprot.org/

Resource of protein sequence and functional information.

  1. Gene Card

http://www.genecards.org

GeneCards is a database of human genes that provides genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes.

  1. Broad-Novartis Cancer Cell Line Encyclopedia (CCLE)

http://www.broadinstitute.org/ccle/home

The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification.

  1. Gene Expression Omnibus

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

A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.

  1. Human Pathway Database

http://discern.uits.iu.edu:8340/HPD/

HPD is an integrated human pathway database providing comprehensive and combined view connecting human proteins, genes, RNAs, enzymes, signaling, metabolic reactions and gene regulatory events.

  1. Allen Brain Atlas

http://www.brain-map.org/

Gene expression in human brains.

  1. Phenologs

http://www.phenologs.org/

Systematic discovery of non-obvious disease models and candidate genes.

  1. Jackson Lab Mouse Resources

http://www.informatics.jax.org/

http://phenome.jax.org/

  1. Transcription factor resources

            General information:

HOCOMOCO

http://autosome.ru/HOCOMOCO/

TFClass

http://tfclass.bioinf.med.uni-goettingen.de/tfclass

SwissRegulon

http://swissregulon.unibas.ch/fcgi/sr/swissregulon

JASPAR – http://jaspar.genereg.net/

Prediction of transcription factor motifs and binding sites:

TRANSFAC – http://www.gene-regulation.com/pub/databases.html

Centipede – http://centipede.uchicago.edu/

Experimental transcription factor binding data

ChIPBase

http://deepbase.sysu.edu.cn/chipbase/

ENCODE

http://genome.ucsc.edu/ENCODE/

  1. StringDB

http://string-db.org/

Database of known and predicted protein interactions. Interactions include direct and indirect associations derived from four sources: genomic context, high-throughput experiments, conserved coexpression, and text-mined published results.

  1. eggNOG

http://eggnog.embl.de/version_4.0.beta/

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes.

  1. Centers for Disease Control and Prevention Public Health Genomics Resources

http://www.cdc.gov/genomics/resources/index.htm

This page contains an A – Z list of Web links to selected genomic resources. These resources are intended for researchers and practitioners, health care providers, health care payers/purchasers, policymakers, and the general public. New links will be added regularly.