As research generates vast amounts of data, it can become overwhelming and make it challenging to know where to begin. Browsers and online platforms for exploring datasets, cohorts, and omics resources are essential research tools that assist researchers in accessing, analyzing, and extracting valuable information from available studies in the PD field.
Here, I highlight some of these resources, but please feel free to comment this if you are familiar with any other to add it to the list!
| Browser/Explorer name | Link | What you can find | Last update |
|---|---|---|---|
| PDGene | http://www.pdgene.org/citing | The PDGene project collected and analyzed data from over 800 genetic association studies on Parkinson’s Disease. In the web page, you can: browse gene details and associations with PD; create your own meta-analysis graphs and reports, visualize GWAS analysis, and explore external links and resources | 2017 |
| GP2 Cohort Browser | https://gp2-cohort-browser-dot-gp2-release-terra.uc.r.appspot.com/ | TheGP2 Cohort Browser is a platform offers comprehensive metadata breakdowns, emphasizes quality control, includes dynamic ancestry analysis, and it provides a dedicated section for rare variants and known PD genes exploration. Future updates will focus on admixture features and SNP metrics. Access requires a tier 2 GP2 data agreement | 2023 |
| Fox Insight Data Exploration Network (Fox DEN) | Fox Insight: Data Exploration Network | Fox DEN is a tool that allows to explore, download, and analyze data collected in the Fox Insight online clinical study, which gathers patient-reported outcomes and genetic data from individuals with PD. Researchers can access questionnaire data related to health, symptoms, and daily activities, genetic data from 23andMe, and microbiome data from participants with and without Parkinson’s. Access requires FOX INSIGHT Data Use Agreement. | 2023 |
| AMP PD Target Explorer | https://target-explorer.amp-pd.org/ | The AMP PD Target Explorer is a resource allows exploring nominated targets such as genes and proteins implicated in PD using data from AMP-PD, including genomics, transcriptomics, and proteomics data. Includes PPMI, PDBP, HBS and BioFIND cohorts | 2023 |
| Foundational Data Initiative for Parkinson’s Disease (FOUNDIN-PD) | FOUNDIN-PD Explorer | The FOUNDIN-PD Atlas interactive tool provides an aggregate-level view of omics data derived from pluripotent stem cells (iPSC) lines obtained from the Parkinson’s Progression Markers Initiative (PPMI). In this platform, you may browse single-cell data or browse assays by genomic position. Use of the portal is subject to a Data Use Agreement | 2023 |
| iPDGC GWAS Locus Browser | GWAS Locus Browser | The iPDGC GWAS Locus Browser is an online platform that gathers diverse data, such as genetic, genomic, and functional information. You can browse any hit from three PD GWAS and explore available information about eQTLs, brain, blood and substantia nigra expression and gene networks, etc. in order to prioritize candidate genes from GWAS. | 2021 |
Also, I want to highlight that some of these tools already have well documented posts in the DCOP page!
For instance, @vdardov made a great post about the AMP PD Target Explorer here
As well, some posts have previously mentioned FoxDEN, like here and here.