Gossypium hirsutum BBH (best bidirectional hit) and OMA homoeolog comparisons

This dataset contains the results for the paper "Homoeolog inference methods requiring bidirectional best hits or synteny miss many pairs."

It contains the following data frames:

• hom_df.csv: All homoeolog pairs inferred from OMA (32426 pairs). Includes pairwise characteristics such as Evolutionary Distance, etc.
• hom_df_with_synteny_scores.csv: all homoeolog pairs for which synteny scores could be computed (31901 pairs). Includes pairwise characteristics such as BBH category, SyntenyScore, Evolutionary Distance, etc.
• gene_centric_df.csv: Nonredundant gene-centric dataframe with expression and other metrics
• tpm_count_goshi.csv: transcripts per kilobase million counts for each gene, using raw RNAseq data from Zhang et al 2015
• Supplemental_Table_4_GO_df.csv: Gene Ontology enrichment for each BBH category, only significant results
• Agenes_vs_Ddb_maxtargetseqs1.blastp: BLASTP results of A subgenome genes as query and D subgenome as database
• Dgenes_vs_Adb_maxtargetseqs1.blastp: BLASTP results of D subgenome genes as query and A subgenome as database
• Homoeolog_BBH_vs_OMA_all_analyses_1Apr2021.ipynb: jupyter notebook containing all analyses (ipython notebook version)
• Homoeolog_BBH_vs_OMA_all_analyses_1Apr2021.html: jupyter notebook containing all analyses (html version)