This is a recipe to make a gene matrix.

1. Clone this repository using git clone https://github.com/mwjjeong/gene-mat-recipe.git
2. Download necessary data by executing src/download.py
3. Execute the cells in src/recipe.ipynb in a given order
4. You can change some settings by editing configuration files in conf/. Here are details of the configuration files.
   • conf/filepaths.yaml lists paths of files used to make a gene matrix. It is not recommended to edit this configuration.
   • conf/fileurls.yaml lists URLs of files to download data used to make a gene matrix. Do not edit this file.
   • conf/gene_biotype.yaml lists gene biotypes with their parent categories defined in the GENCODE v33. Do not edit this file.
   • conf/gene_list_names lists column names of a gene matrix. You can edit the values if you want to change column names.
   • Note: Do not edit the keys of all the configuration files.

• ASD associated genes (FDR≤0.1)
• ASD associated genes (FDR≤0.3)
• Midfetal co-expression genes
• Constrained genes (pLI ≥ 0.9)
• Postsynaptic density genes
• Developmental delay genes
• Brain expressed genes
• CHD8 targets
• FMRP targets

• Protein coding genes
• Long ncRNAs
• Small ncRNAs
• Pseudogenes
• IG/TR genes

• 102 ASD genes (Satterstrom et al., Cell, 2020)
• 299 DDD genes
• Haploinsufficient genes (gnomAD pLI ≥ 0.9)
• Haploinsufficient genes (gnomAD pLI ≥ 0.995)
• Genes in WGCNA modules associated with ASD (Parikshak et al., Nature, 2016)
  • RNA-seq of 251 post-mortem samples of frontal and temporal cortex and cerebellum from 48 individuals with ASD and 49 control subjects
  • Identified 6 modules significantly associated with ASD of 24 modules from WGCNA
    • Upregulated: CTX.M9, CTX.M19, CTX.M20
    • Downregulated: CTX.M4, CTX.M10, CTX.M16
• Marker genes of cell clusters from scRNA-seq (Nowakowski et al., Science, 2017)
  • scRNA-seq of samples from primary cortical and medial ganglionic eminence (MGE) in developing human telencephalon
  • 5.85 ~ 37 PCW
  • Unbiased clustering and found marker genes for each cluster
  • Transcriptionally distinct cell clusters corresponding to 11 broad categories: astrocytes, oligodendrocyte precursor cells, microglia, radial glia, intermediate progenitor cells, excitatory cortical neurons, ventral MGE progenitors, inhibitory cortical interneurons, choroid plexus cells, mural cells, and endothelial cells
• Marker genes of cell clusters from scRNA-seq (Li et al., Science, 2018)
  • scRNA-seq of 9 de-identified postmortem brains (Table S3)
  • 5 PCW ~ 20 PCW
  • Marker genes for each cell type of Pallium, CP, DFC, NCX regions in a human brain
• Marker genes of cell clusters from snRNA-seq (Velmeshev et al., Science, 2019)
  • snRNA-seq
  • 41 post-mortem tissue samples including prefrontal cortex (PFC) and anterior cingulate cortex (ACC) from 16 controls and 15 ASD patients.