Aggregating gut: on the link between neurodegeneration and bacterial functional amyloids - Datasets

This repository contains data from work "Aggregating gut: on the link between neurodegeneration and bacterial functional amyloids"

BFA.fasta - fasta file containing sequences of bacterial functional amyloids used as a query for identification of novel bacterial functional amyloids in UHGP dataset

UHGPAmyloids.fasta - fasta file containing sequences of amyloids identified in UHGP dataset

UHGPAmyloids.csv - csv file containing information about amyloids identified in UHGP

Columns:
query_id - Uniprot id of the protein from BFA
query_gene_name - gene name of the protein from BFA
target_id - UHGP id of the found homolog
ProbabilityAMYPred-FRL - score obtained for the target_id sequence according to AMYPred-FRL
Archcandy - Prediction of beta arch motif for identified amyloid
Genome - UHGP genome id of the target_id
Localization - predicted subcellular localization with BUSCA for target_id sequence
Lineage - full taxonomy of the target_id sequence (which bacteria produced this specific sequence) 

PPIPositivePredictionsBetween_UHGPAmyloids_And_HPAIntestine_filtered.csv - csv file contining inforamtions about predicted protein-protein interactions between UHGPAmyloids and human proteins expressed in guts

Columns:
UHGPAmyloids_id - UHGPAmyloids id (same as target_id in UHGPAmyloids.csv)
hp_uniprot_name - Uniprot name of a human protein
negative and score - scores returned by ProteinPrompt softwawre for prediction of PPI
hp_uniprot_id - Uniprot id of a human protein
BFA_sp_uniprot_id - Uniprot id of a BFA source protein
BFA_sp_uniprot_name - gene name of a BFA source protein
UHGPAmyloids_localization  - predicted subcellular localization with BUSCA for UHGPAmyloids_id sequence
UHGPAmyloids_lineage - full taxonomy of the UHGPAmyloids_id sequence (which bacteria produced this specific sequence)