Input datasets for Systems-level transcriptomics reveals regulatory networks and candidate genes underlying the post-pollination syndrome in Vanilla planifolia

The input datasets used in this study correspond to the files associated with each analytical step implemented in the repository: https://github.com/Andrea-H-M/SystemsLevel_transcriptomics/tree/main These inputs include DEG lists from Arabidopsis thaliana, Solanum lycopersicum, Vitis vinifera, and Vanilla planifolia; FASTA sequence files used for orthology inference; gene identifier lists; transcription factor (TF) and epigenetic regulator (EpiReg) reference tables; expression matrices and annotated count tables used for WGCNA and hub gene identification; KEGG Orthology (KO) annotation files; binary transcriptional label matrices; and module-specific gene lists used for transcriptional label integration and candidate regulator prioritization. The repository structure preserves the workflow organization described in the Methods section of the manuscript, linking each script with its corresponding input files required to reproduce orthology inference, functional enrichment, co-expression network analyses, transcriptional label integration, and candidate regulator prioritization associated with the flower-to-fruit transition and post-pollination syndrome in Vanilla planifolia.