This directory contains supplementary material for Taiwanese trio manuscript.

The BioArxiv manuscript is available here: https://www.biorxiv.org/content/early/2018/12/13/495036

This directory provides tab separated tables in place of excel spreadsheets, as .xls formatting often overwrites particular gene symbols as dates.
Tab separated files (.tsv) are formatted to have no empty lines and ready for analysis
Comma separated files (.csv) are unstructured tables for viewing

NOTE: The descriptions of each column for the files listed below are available in sheet_descriptions.csv

PDF files:

Taiwanese-trio_Supplement_BioArxiv.pdf - supplementary information and figures

Tab separated Files (.tsv):

taiwanese_cohort_sample_list.tsv - per sample phenotype and sequence summary information
taiwanese_cohort_trio_list.tsv - per-trio phenotype and sequence summary information
taiwanese_cohort_DNM_list.tsv - QCed de novo mutation list for Taiwanese Trio cohort (n=1695, hg19 genome reference)
combined_cohorts_DNM_list.tsv - de novo mutation list for SCZ and control trios analyzed in manuscript 
Candidate_gene_set_results.tsv - full gene set enrichment results for all candidate gene sets

Comma separated files (.csv):

sheet_descriptions.csv - column names and descriptions for each file
DNM_studies.csv - Counts and notes of exome-sequenced trios analyzed in the current study
SCZ_DNM_counts.csv - counts and rates of DNM calls in SCZ trio studies
Candidate_gene_sets.csv - 85 candidate gene sets analyzed for gene set enrichment
GO+SynaptomeDB_enrichment.csv - GO and SynaptomeDB terms with p-value < 0.01
Recurrent_PTV_genes.csv - list of genes hit by multiple PTV DNMs
Recurrent_PTV+Missense_genes.csv - list of genes hit by multiple PTV or Missense DNMs
Gene_recurrence_by_gene_sets.csv - Gene recurrence permutation test among highly brain expressed and constrained genes
Predicted_SCZ_risk_genes.csv - Estimation of SCZ risk genes from recurrence rate of PTV or PTV/Missense DNMs in SCZ probands