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)