EBV T cell antigen Database -- FAQ

Questions

1. How many antigens are there in EBVdB?
2. How were T cell epitopes and HLA ligands defined in EBVdB?
3. How do I get information on an EBV antigen of my interest?
4. How to search for T cell epitopes or HLA ligands?
5. I have an antigen sequence with unknown functions. How do I get more information on this sequence?
6. How do I get a global view of all the experimentally validated T cell epitopes and HLA ligands in an antigen sequence?
7. How do I get a global view of all the experimentally validated T cell epitopes and HLA ligands in all the variants of an antigen?
8. How do I view all the experimentally validated T cell epitopes and HLA ligands in an antigen sequence and get information on their restricted HLA alleles at the same time?
9. How do I view sequence variability of EBV proteins?
10. What information does an antigen entry table provide?
11. What information does an antigen entry table provide?

Answers

1. EBV DB version 1.0 consists of 900 curated antigen entries of antigenic proteins encoded from EBV genome. These proteins were derived form 444 EBV strains. See classification page for details.

   
   
   [Go Back]

2. In building EBV DB, the criterion for antigenic selection of EBV T cell antigens is that antigens must either be presented by one or more HLA alleles or be recognized by T cells through experimental validation. If a peptide had the ability to stimulate T cell function, it was called "T cell epitope". If a peptide only had binding affinity measured or was directly eluted and analyzed by mass spectrometry without activation of T cells, this peptide was called "HLA ligand". Currently this database contains 190 T cell epitopes but no HLA ligands.
   
   [Go Back]

3. To get information on antigens of your interest, go to Search page, select "Search Antigen Records" and input an antigen name into the text box. If nothing was input into the text box, the search result page will show all the antigens in the database. In the below example figure, the user input antigen name is "LMP1".
   
   

   The search results are displayed into table as shown in below figure. Click on an accession number to go to an antigen entry table for detailed information.
   
   
   
   [Go Back]

4. To get information on T cell epitopes or HLA ligands, go to Search page, select "Search T cell epitopes/HLA ligands" and input either an epitope/ligand sequence or an HLA allele of your interest in the text box. If nothing was input into the text box, the search result page will show all the T cell epitopes and HLA ligands in the database. In below example figure, the user input "A24".
   
   

   The search results are displayed into table as shown in below figure. Click on an accession number to go to an epitope or ligand table for detailed information.
   
   
   
   [Go Back]

5. If you have an amino acid sequence and would like to get more information on it, you can use BLAST function to search for similar antigen sequences in EBV DB.
   
   

   On the BLAST result page, you can also select several antigen sequences of your interest and align them with your input sequence.
   
   
   
   
   
   [Go Back]

6. Go to View Epitope page, select "Format 1", and select an antigen name and EBV genotype in the selection box. Below is the result page with all the epitope and ligands highlighted in the antigen sequence.
   
   [Go Back]

7. Go to View Epitope page, select "Format 2", and select an antigen name and EBV genotype in the selection box. Below result page shows the multiple sequence alignment of all isoforms of antigen BZLF1 with the epitope and ligands highlighted.
   
   [Go Back]

8. Go to View Epitope page, select "Format 3", and select an antigen name and EBV genotype in the selection box. Below result page shows the sequences of antigen BZLF1 with all the epitope/ligands and their restricted HLA alleles listed below the sequences.
   
   [Go Back]

9. Go to Alignment page, select protein and virus genotype in the selection box.
   
   
   
   [Go Back]

10. An antigen record table provides below information:

    EBVACC	Unique accession number for an antigen record in EBV DB
    Date	Entry date of the record
    Last updated date	Latest date of information update on the entry
    Antigen Name	Protein name
    Full Name	Complete protein names from Uniprot or Genbank
    Synonym	Other protein names or gene names of the antigen
    Virus strain	Name of virus strain according to EBV study
    Genotype	Virus genotype
    UniProt ID or NCBI ID	Cross-references to corresponding record in Uniprot database or GenBank protein database
    T cell epitope	Epitope sequence	Position	HLA allele	Reference
    	T cell epitope sequence	Position of the epitope in the antigen sequence	restricted HLA allele	PubMed link of the paper containing the T cell epitope validation result
    HLA ligand	Ligand Sequence	Position	HLA allele	Reference
    	HLA ligand sequence	Position of the ligand in the antigen sequence	restricted HLA allele	PubMed link of the paper containing the HLA ligand binding result
    Predicted HLA binders	Prediction of 9-mer peptide binding affinities to 15 HLA Class I and Class II alleles, A*0101, A*0201, A*0301, A*1101, A*2402, B*0702, B*0801, B*1501, DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1301, and DRB1*1501.
    Antigen sequence	Protein sequence of the antigen

    
    
    [Go Back]