Matlab Codes and sample data for our paper: "Systematic analysis of gene expression patterns associated with postmortem interval in human tissues"
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Make sure your version of MATLAB software is at least 2013.
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Edit file paths (e.g., the HOMEPATH) in the scripts based on your settings.
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Unzip the data.zip. The folder contains all necessary sample data (Adipose_Subcutaneous) for reproducing the results (part 1 and 4) in our paper.
- genelist.mat --- 18763 Protein Coding Genes
- expr_Adipose_Subcutaneous_159_144.mat --- Gene expression matrix
- cov_Adipose_Subcutaneous_159_144.mat --- Covariates
- peer_Adipose_Subcutaneous_159_144.mat --- PEER algorithm to infer the hidden data structures
- smpl_Adipose_Subcutaneous_159_144.mat --- Subject-level variables, including age, gender, BMI, etc., and sample-level variable (PMI)
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Directly run linear_res/s1_res_regr.m first and then s2_extract_sig_fdr_gene_list.m to identify PMI-associated genes (part 1, results).
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Directly run PMI_dispersion/s1_levene_test_p_values.m first and then s2_extract_fdr_genes.m to identify PMI-associated DV genes (part 4, results).
Note that we did not attach the genotype data in the PMI-by-genotype analyses, due to the data privacy of the GTEx project. All the data is available upon request from dbGaP (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v6.p1).
A manuscript detailing our work has been accepted by Scientific Reports:
Y. Zhu, Y. Yin and E. Yang (2017) Systematic analysis of gene expression patterns associated with postmortem interval in human tissues (http://www.nature.com/articles/s41598-017-05882-0).
Contact: zhuyizhang@bjmu.edu.cn