TANTIGEN -- FAQ

Questions

1. How many antigens are there in TANTIGEN?
2. How are T cell epitopes and HLA ligands defined in TANTIGEN?
3. How can I list all the names of antigens in TANTIGEN?
4. How do I get information on an cancer antigen of my interest?
5. How do I search for T cell epitopes or HLA ligands?
6. I have an antigen sequence with unknown function. How do I get more information on this sequence?
7. How are the antigens in TANTIGEN classified?
8. How do I get a global view of all the experimentally validated T cell epitopes and HLA ligands in an antigen sequence?
9. 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?
10. 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?
11. What information does an antigen entry table provide?
12. What is our nomenclature for splice isoform names?
13. Who should I contact if I have more questions?

Answers

1. TANTIGEN hosts more than 1000 tumor peptides from 292 different proteins. All peptides in TANTIGEN are labelled as one of four categories: 1) peptides measured in vitro to bind the HLA, but unable to elicit either in vivo or in vitro T cell response, 2) peptides found to bind the HLA and to elicit an in vitro T cell response, 3) peptides shown to elicit in vivo tumor rejection, and 4) peptides processed and naturally presented as defined by physical detection. In addition to T cell response, we also annotate peptides that are naturally processed HLA binders, e.g. peptides eluted from HLA in mass spectrometry studies.

   Genomic origin	Proteins	In vitro T cell epitopes	In vivo T cell epitopes	HLA ligands	MS derived HLA ligands	Total peptides
   Substitution mutation (neoepitopes)	63	43	11	48	8	110
   Alternative ORF	4	10	0	0	0	10
   Intron encoding	1	2	0	0	0	2
   Chromosomal translocation	10	30	0	17	0	47
   Internal tandem repeat	1	1	0	0	0	1
   Differentiation	16	131	4	8	3	146
   Overexpressed	82	237	9	257	13	516
   Shared tumor specific	35	147	0	2	3	152
   Unclassified	80	123	1	25	11	160
   Total	292	724	25	357	38	1144

   
   
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2. TANTIGEN contains peptide entries representing peptides experimentally shown to bind one or more HLA alleles (HLA ligands) or that were recognized by T cells in functional assays (T cell epitopes).
   
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3. You can obtain all the names and synonyms of the antigens in the database on nomenclature page.
   
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4. 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 below example figure, the user input antigen name is "survivin".
   
   
   
   The search result table is displayed as shown in the below figure. Antigen name column shows protein symbols according to HUGO Gene Nomenclature Committee. Common name is the name frequently use by tumor immunologists or oncologists. Comment column displays either isoform names or some commentary information such as, putative, substitution mutation, alternative ORF, chromosomal translocation, etc. Click on an accession number to go to an antigen entry table for detailed information.
   
   
   
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5. 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 "A*0301".
   
   
   
   The search results are displayed into two tables as shown in the below figure. The top table displays T cell epitopes and the bottom one HLA ligands. Click on an accession number to go to an epitope or ligand table for detailed information.
   
   
   
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6. 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 TANTIGEN.
   
   
   
   On the BLAST result page, you can also select several antigen sequences of your interest and align them with your input sequence.
   
   
   
   
   
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7. Go to classification page. In the classification diagram, by clicking on a name of a tumor antigen, you will get all the variants of this antigen. For example, below result page shows all the entries of antigen BRAF.
   
   
   
   
   
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8. Go to View Epitope page, select "Format 1", and input an antigen name or a TANTIGEN accession number into the text box. Below is the result page with all the epitope and ligands highlighted in the antigen sequence.
   
   
   
   
   
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9. Go to View Epitope page, select "Format 2", and input an antigen name into the text box. Below result page shows the multiple sequence alignment of all isoforms of antigen BIRC5 with all the epitope and ligands highlighted in the sequences.
   
   
   
   
   
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10. Go to View Epitope page, select "Format 3", and input an antigen name into the text box. Below result page shows the sequences of antigen BIRC5 with all the epitope/ligands and their restricted HLA alleles listed below the sequences.
    
    
    
    
    
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11. An antigen record table provides below information:

    AgACC	Unique accession number for an antigen record in TANTIGEN
    Date	Entry date of the record
    Last updated	Latest date of information update on the record
    Antigen Name	Protein name based on HUGO gene nomenclature guidelines
    Common Name	Name of antigens used in tumor immunology filed
    Full Name	Complete protein name from GeneCard or literature
    Synonym	Other protein names or gene names of the antigen
    Isoform Name	Systematic name of alternative products assigned by TANTIGEN (only available for full length antigen sequences)
    UniProt ID	Cross-references to corresponding record in Uniprot databases if available
    NCBI Gene ID	Cross-references to corresponding record in NCBI Gene databases if available
    GeneCard ID	Cross-references to corresponding record in GeneCard databases if available
    COSMIC ID	Cross-references to corresponding record in Catalogue of Somatic Mutations in Cancer (only available in some substitution mutation entries)
    SwissProt VARIANT ID	Cross-references to corresponding SwissProt variant page (only available in some substitution mutation entries)
    Comment	Comment on the antigen if available
    Annotation	Annotation on antigen sequence type: full length sequence or fragment
    COSMIC ID	Cross-reference to corresponding record in Catalogue of Somatic Mutations in Cancer (only available in some substitution mutation entries)
    Gene expression profile	Gene expression profile suggested by analysis of EST counts from Unigene
    Isoforms	Accession numbers of its isoforms and comparison of the isoforms sequences using multiple sequence alignment
    Mutation entries	Accession numbers of substitution mutations and visualize single amino acid change using mutation map
    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.
    Reference sequence	Protein sequence before substitution mutation (only available in substitution mutation entries)
    Antigen sequence	Protein sequence of the antigen

    
    
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12. Splice isoform names were assigned only to full length antigen sequences based on human gene nomenclature guideline (HGNC). An isoform name starts with a protein symbol, followed by an underscore, a letter "i", and a number representing which isoform it is, for example BIRC5_i1. If there are several sequence variations belonging to the same isoform, their isoform names are extended by an underscore, a letter "v" together with numbers representing the variations, for example BIRC5_i1_v1.
    
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13. For further information and questions, please contact: Guanglan Zhang or Vladimir Brusic.
    
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