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Files

NameDescriptionDownload
NDAtlas PPI networkIt is the PPI network file of NDAtlas in cyjs format for network analysis in Cytoscape.Download
Protein docking scoresThe protein docking score file in plain text format represents the structural affinity of docking proteins.Download
Disease termsThis file contains the related neurodegnerative disease terms in NDAtlas.Download
Disease involved proteinsReviewed proteins involved in neurodegnerative diseases.Download
Gene ontology enrichmentThe file with .bgo extension includes the gene ontology (GO) enrichment on neurodegnerative related pathwaysDownload

README

Information of NDAtlas Data Files

This page contains data files related to NDAtlas, a web-based platform for exploring neurodegenerative diseases. The details of the files:

NDAtlas PPI network

This file in cyjs format contains the network data of NDAtlas, which can be imported into Cytoscape, a software for network analysis and visualization. The network data consists of nodes (proteins) and edges (interactions) annotated with various attributes, such as disease association, pathway membership, and protein function. To import the file into Cytoscape, follow these steps:

  • Download the file from the link below and save it to your local directory. If necessary, change the filename extension to "cyjs", rather than "txt".
  • Open Cytoscape and go to File > Import > Network from File.
  • Select the downloaded file and click Open.
  • Adjust the network layout and style in your need.
  • Explore the network data using Cytoscape tools and features.

Protein docking scores

This file contains the protein docking scores of NDAtlas proteins, which represent the structural affinity of docking proteins. The docking scores are calculated using ZDOCK, a protein-protein docking algorithm. The plain text file is in tab-delimited format, with each row representing a pair of proteins and each column representing a docking score. The higher the score, the more likely the proteins are to interact. To view the file, you can use any text editor or spreadsheet software.

PDB1PDB2docking score
PDB ID of protein 1PDB ID of protein 2The docking score calculated on the interaction pair

Disease terms

This file contains the related neurodegenerative disease terms in NDAtlas, which are extracted from various sources, such as MeSH, OMIM, and disease ontology (DO). The plain text file is in tab-delimited format, with each row representing a disease term and each column representing an attribute, such as name, ID, abbreviation, and synonyms. To match the disease terms with NDAtlas proteins or pathways, you can use the search function on the NDAtlas website.

disease_iddisease_labeldisease_namedisease_uniprotdomesh
The disease identifier in NDAtlasThe abbreviated label of the diseaseThe formal name of the diseaseThe UniProt entry ID of the diseaseDisease Ontology identifierMeSH identifier

Disease involved proteins

This file contains the reviewed proteins involved in neurodegenerative diseases curated from UniProt. The plain text file is in tab-delimited format, with each row representing a protein and each column representing an attribute, such as UniProt ID, disease label, and all diseases this protein is involved.

uniprotinv_diseaseinv_disease_detail
UniProt ID of proteinThe abbreviated label of disease the protein is involved. "C" means multiple diseases have the protein in common.The abbreviated label of disease the protein is involved. What diseases have the protein in common are shown in detail, joined with '-'.

GO Enrichment

This bgo file contains the enrichment results of NDAtlas proteins on neurodegenerative related pathways, which are derived from BINGO. If necessary, change the filename extension to "bgo", rather than "txt". The file is in tab-delimited format, with each row representing a pathway and each column representing an enrichment statistic, such as name, ID, p-value, and fold change. To view the file, you can use any text editor or spreadsheet software. To visualize the enrichment results on NDAtlas network or pathways, you can use any network or pathway visualization tool.