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 BFAquery_gene_name - gene name of the protein from BFAtarget_id - UHGP id of the found homologProbabilityAMYPred-FRL - score obtained for the target_id sequence according to AMYPred-FRLArchcandy - Prediction of beta arch motif for identified amyloidGenome - UHGP genome id of the target_idLocalization - predicted subcellular localization with BUSCA for target_id sequenceLineage - 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 proteinnegative and score - scores returned by ProteinPrompt softwawre for prediction of PPIhp_uniprot_id - Uniprot id of a human proteinBFA_sp_uniprot_id - Uniprot id of a BFA source proteinBFA_sp_uniprot_name - gene name of a BFA source proteinUHGPAmyloids_localization  - predicted subcellular localization with BUSCA for UHGPAmyloids_id sequenceUHGPAmyloids_lineage - full taxonomy of the UHGPAmyloids_id sequence (which bacteria produced this specific sequence)

本仓库收录了研究论文《Aggregating gut: 神经退行性疾病与细菌功能性淀粉样蛋白之间的关联》的相关实验数据。

BFA.fasta：FASTA格式文件，包含作为查询集的细菌功能性淀粉样蛋白（bacterial functional amyloids）序列，用于在UHGP数据集内识别新型细菌功能性淀粉样蛋白。

UHGPAmyloids.fasta：FASTA格式文件，包含在UHGP数据集中识别到的淀粉样蛋白序列。

UHGPAmyloids.csv：CSV格式文件，包含在UHGP数据集中识别到的淀粉样蛋白的相关信息。各字段说明如下：
- query_id：来源BFA的蛋白质的UniProt编号
- query_gene_name：来源BFA的蛋白质的基因名称
- target_id：所发现同源蛋白的UHGP编号
- ProbabilityAMYPred-FRL：基于AMYPred-FRL模型对target_id序列计算得到的预测评分
- Archcandy：对所识别淀粉样蛋白的β折叠螺旋基序的预测结果
- Genome：target_id对应的UHGP基因组编号
- Localization：基于BUSCA工具对target_id序列预测得到的亚细胞定位信息
- Lineage：target_id序列所属细菌的完整分类学信息（即该序列产生的具体细菌类群）

PPIPositivePredictionsBetween_UHGPAmyloids_And_HPAIntestine_filtered.csv：CSV格式文件，包含UHGP淀粉样蛋白与肠道表达的人类蛋白质之间预测得到的蛋白质-蛋白质相互作用（Protein-Protein Interaction, PPI）相关信息。各字段说明如下：
- UHGPAmyloids_id：UHGPA淀粉样蛋白的编号（与UHGPAmyloids.csv中的target_id字段完全一致）
- hp_uniprot_name：人类蛋白质的UniProt名称
- negative and score：由ProteinPrompt软件预测蛋白质相互作用时返回的评分
- hp_uniprot_id：人类蛋白质的UniProt编号
- BFA_sp_uniprot_id：BFA来源蛋白质的UniProt编号
- BFA_sp_uniprot_name：BFA来源蛋白质的基因名称
- UHGPAmyloids_localization：基于BUSCA工具对UHGPAmyloids_id序列预测得到的亚细胞定位信息
- UHGPAmyloids_lineage：UHGPAmyloids_id序列所属细菌的完整分类学信息（即该序列产生的具体细菌类群）