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Research demonstrates a protein language model defines the pangenome landscape, indicating its role in regulating proteostasis in E. coli strains.
Extended Data for the Article: A protein language model unveils the E. coli pangenome functional landscape regulating host proteostasis Summary: libraries-barcodes: barcodes and associated metadata used to demultiplex the C. elegans RNA-seq for the mono-association experiments between E. coli strains and C. elegans RNA_lexogen_worm_norm_batch: DESeq2 normalised and batch corrected counts for the RNA-seq data experiment. MAIN_ecoli_NCBI_metadata: complete metadata of the 9558 E. coli strains used in the article. gene_presence_absence.Rtab: Panaroo-generated file with the presence/absence matrix of the 9558 strains pan_genome_reference(_aa)_TOTAL: Panaroo-generated file with the linear reference of the nucleotide or amino acid sequences of the gene families found in the pangenome gene_t5_embeddings_METADATA_FINAL: protein embeddings from the linear representation of the amino acids from the pangenome. PG_full_core_tree.treefile/PG_lexogen_core_tree.treefile: tree files to recreate the phylogenetic representation in the article. strain_embeddings_(ADDITION/AVERAGE/WEIGHTED_AVERAGE): strain embedding representation from the 9558 strains calculated following 3 different methodologies.
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Martínez-Martínez et al. (2029) studied this question.
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