Resources
Network browser of AD proteomic consensus network from Swarup, Chang et al. Identification of conserved proteomic networks in neurodegenerative dementia. Cell Reports 2020.
A web-based browser that permits querying by gene or by cell type for expression during human brain development. From Polioudakis, de la Torre-Ubieta et al. A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation. Neuron 2019.
A web tool for determining the composition and stage of stem cell-based neuronal models in a dish. from Stein et al., A Quantitative Framework to Evaluate Modeling of Cortical Development by Neural Stem Cells. Neuron 2014.
A companion browser to the developing human brain eQTL and sQTL resource from Walker et al. Genetic control of expression and splicing in developing human brain informs disease mechanisms. Cell 2019. Download all significant eQTL by SNPs.
A web-based browser that for exploring gene expression trajectories during long term cortical organoid differentiation and in vivo brain development. From Gordon et al. Long-term maturation of human cortical organoids matches key early postnatal transitions. Nature Neuroscience 2021.
An interactive human brain development co-expression network plot from Parikshak et al. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell 2013.
Visual browser of the PsychENCODE transcriptome network capstone data. From Gandal et al. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science 2018.
Download tutorials on the ATAC-seq protocol (Word document).
CWOW aims to use multi-omics and functional genomic CRISPR screens to understand the differences in gene expression and cellular function as a result of the MAPT H1/H2 haplotype inversion, its effects on sporadic and familial tauopathies, and identification of novel therapeutic targets for the treatment of tauopathies.
MSigDB gene set collections, including pathway and transcription factor gene sets.
General resources for the PsychENCODE consortium.
SSPsyGene aims to understand the impacts of mutations for over 200 genes known to contribute to neuropsychiatric and neurodevelopmental disease risk. Through a high throughput, quantitative, and multi-scale pipeline, the program will generate cell lines with mutations for each gene of interest and characterize the effects of mutation on human cortical development using 2D and 3D platforms.
A tool for Transcription Factor binding predictions from transcriptional networks.
Tutorials on using WGCNA, a software package containing a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis.
Program of Neurogenetics
