| Name | Description | Download |
|---|---|---|
| NDAtlas PPI network | It is the PPI network file of NDAtlas in cyjs format for network analysis in Cytoscape. | Download |
| Protein docking scores | The protein docking score file in plain text format represents the structural affinity of docking proteins. | Download |
| Disease terms | This file contains the related neurodegnerative disease terms in NDAtlas. | Download |
| Disease involved proteins | Reviewed proteins involved in neurodegnerative diseases. | Download |
| Gene ontology enrichment | The file with .bgo extension includes the gene ontology (GO) enrichment on neurodegnerative related pathways | Download |
This page contains data files related to NDAtlas, a web-based platform for exploring neurodegenerative diseases. The details of the files:
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:
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.
| PDB1 | PDB2 | docking score |
|---|---|---|
| PDB ID of protein 1 | PDB ID of protein 2 | The docking score calculated on the interaction pair |
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_id | disease_label | disease_name | disease_uniprot | do | mesh |
|---|---|---|---|---|---|
| The disease identifier in NDAtlas | The abbreviated label of the disease | The formal name of the disease | The UniProt entry ID of the disease | Disease Ontology identifier | MeSH identifier |
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.
| uniprot | inv_disease | inv_disease_detail |
|---|---|---|
| UniProt ID of protein | The 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 '-'. |
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.