Alpha1 – HDinHD

HD Explorer

Disease Signatures

GWAS & DNA Repair

Mouse Allelic Series

Data Analysis

A cross-sectional mouse in-vivo project developed collaboratively between MGH, Psychogenics (PGI) and CHDI. RNAseq, proteomics and behavioural data were generated from both central and peripheral tissue of both WT and an allelic series of HD model mice Q20, Q80, Q92, Q111, Q140, Q175 at 2, 6 and 10 months of age. Data was then subject to differential expression analysis and causal modeling.

Credits: Data Analysis Rancho BioSciences. Causal modeling by AITIA (formerly GNS HealthCare).
Mouse Allelic Series project conception and execution: MGH, PsychoGenics (PGI) and CHDI.

HD Explorer	Integrated network of HD experimental data curated and analyzed from the literature, community ‘omics repositories and newly-released internal CHDI reports.
Download HD Explorer Data	Download component datasets from HD Explorer, including HDSigDB, an HD-relevant gene set enrichment library designed to provide rich functional context for HD-related gene set enrichment analysis.
Download HD Disease Signatures	A 266 striatal gene HD disease signature and a 115 striatal protein HD disease signature were developed through analysis of Mouse Allelic Series data and validated in external datasets. Link to a bioRxiv manuscript describing this work, or download manuscript and supplement files directly.
GeM MOA SNP Viewer	Summary findings from Huntington's disease genome-wide association studies that seek out genes that influence the pathogenesis and expression of Huntington’s disease
GeM Euro 9K	Visualization tools and summary results of a genome-wide association study to identify genetic modifiers of Huntington's disease conducted by the GeM-HD Consortium (PMID: 31398342 and 34180418)
Download GWAS Gene Reports	Gene reports generated on genes under peaks implicated in early GWAS analyses.
Download DNA Repair & Handling Reports	A topic report (2016) identifying and articulating the genes and pathways involved in DNA damage and repair, with an emphasis of Huntington’s Disease and other trinucleotide disorders. Visual and computational pathway maps are included for DNA Mismatch Repair, Base Excision Repair, Nucleotide Excision Repair and Inter-Strand Crosslink Repair.
Download Mouse Allelic Series DEG Results	Download differential gene and protein expression results from central and peripheral tissues generated within a cross-sectional mouse in-vivo project of both WT and an allelic series of HD model mice with increasingly long CAG repeats (Q20, Q80, Q92, Q111, Q140, Q175) at 2, 6 and 10 months of age. Behavioural data is also available for download.
Download Mouse Allelic Series Causal Modeling Results	Gene reports generated on genes under peaks implicated in early GWAS analyses.
ASViewer	Visualize Q-length and age dependent gene and protein expression data from central and peripheral tissue of the cross-sectional Mouse Allelic Series project at both the aggregate (grouped by genotype) and individual animal level. New in v1.9: CAG length data (from tail or ear) now included for hundreds of individual animals.
CoExMap Viewer	Visualization tool allowing exploration of results and underlying data of a large scale Weighted Gene Co-expression Network Analysis (WGCNA) of hundreds of samples from intact mouse striatum at 6-month of age as well as from gene set enrichment analysis of transcriptomic signatures of differentially expressed genes from 52 heterozygous HD knockout mice and wildtype controls.
Brain-C Lab HD Knowledge Base	A suite of precision machine learning tools for Huntington’s disease research.
Adult Astrocyte RNAseq Explorer	Visualize Astrocyte gene expression profiles across brain regions and HD disease models
EnrichR	Gene set enrichment analysis tool operating over a large and diverse collection of gene set libraries including HDSigDB, a gene set library containing HD and HD-related gene sets.