DM Potato (v6.1) Gene Coexpression

Gene co-expression analyses were performed across 440 RNA-seq libraries that are grouped into 18 tissues or conditions. Co-expression modules were constructed as described in Li et al., 2023 (PMID: 37063055) using gene expression (transcript per million, TPM) abundances generated with Kallisto (PMID: 27043002) with the DM v6.1 representative gene models. TPM values were log-transformed, and biological replicates were averaged to calculate z-scores. Genes with no expression in any tissue were removed prior to downstream analyses. All pair-wise correlations were performed on the remaining 36,025 genes. To build the correlation network edge table, only edges with r > 0.8 were used, which corresponded to the top 1% of all edges. A network object was constructed using the 'graph_from_data_frame()' function of igraph. Graph based clustering was performed using the Leiden algorithm (implemented as the 'cluster_leiden()' function in R as part of the igraph package) with a resolution parameter of 4.

A total of 65 coexpression modules were generated with module sizes ranging between 5 to 2,943 genes.

Download the complete gene coexpression module assignments for all DM Potato (v6.1) genes:

• DM_1-3_516_R44_potato.v6.1.coexpression_modules.txt.gz - Gene coexpression module assignments for all genes
• DM_1-3_516_R44_potato.v6.1.coexpression_modules.xlsx - Gene coexpression module assignments for all genes, Excel format
• DM_1-3_516_R44_potato.v6.1.coexpression_module_list.txt.gz - List of all coexpression modules
• DM_1-3_516_R44_potato.v6.1.coexpression_module_list.xlsx - List of all coexpression modules, Excel format