TBAdb

TBAdb

An introduction of TBAdb database


TBAdb is a manually curated database of T-cell receptor (TCR) and B-cell receptor (BCR) targeting specific antigen or diseases.

The database contains three parts, namely TCR-AB, TCR-GD and BCR. These three parts are aimed at collecting sequences and specificity information of TCRA and TCRB, TCR- gamma and TCR-delta and BCR separately.

Our mission is to present the accurate relationship between TCR/BCR and antigens of diseases in a humanized manner. Therefore, in addition to a broad collection and irregularities correction of articles (early since 1990), many other processes also contribute to the goal:

The detailed information, including disease ICD code, sequencing platform, the method used to identify the specificities and so on, is collected.

The exporting of V/J fragments and CDR3 sequences have been double-checked manually to ensure them stand and correct.

In order to help users to obtain specificities of sequence, the experiments in article are grading as showed in the tutorial document.

The code of V/J fragments are standardized following the IMGT to our best.

The format of CDR3 sequences are ruled with starting with (YX)C in V gene region and ending with W or F(GXG) in the J gene region.

The website provides a series of convenient tools to browse, query, stat and visualize the information. A tutorial document is open to download; it will help you to unitize the database.

1. ICDname:the disease ID of International Classification of Disease (ICD) 10th, which the sequence is correlated to.

2. Disease.name:disease which sequences are special to.

3. Category: the category of the disease.

4. Antigen: the amino acid sequence of antigen.

5. Antigen.sequence:the amino acid sequence of antigen.

6. HLA: the type of leukocyte antigen (HLA) of the sample.

7. Locus: the single chain, such as TRA, TRB, TRD, TRG, IGH, IGK, IGL.

8. CDR3.alpha.aa: the amino acid sequence of complementarity determining region 3 (CDR3) for the TCR sequence alpha chain.

9. CDR3.alpha.nt: the nucleotide sequence of complementarity determining region 3 (CDR3) for the TCR sequence alpha chain.

10. CDR3.beta.aa:the amino acid sequence of complementarity determining region 3 (CDR3) for the TCR sequence beta chain.

11. CDR3.beta.nt:the nucleotide sequence of complementarity determining region 3 (CDR3) for the TCR sequence beta chain.

12. CDR3.gamma.aa: the amino acid sequence of complementarity determining region 3 (CDR3) for the TCR sequence gamma chain.

13. CDR3.gamma.nt: the nucleotide sequence of complementarity determining region 3 (CDR3) for the TCR sequence gamma chain.

14. CDR3.delta.aa: the amino acid sequence of complementarity determining region 3 (CDR3) for the TCR sequence delta chain.

15. CDR3.delta.nt: the nucleotide sequence of complementarity determining region 3 (CDR3) for the TCR sequence delta chain.

16. CDR3.light.aa:the amino acid sequence of complementarity determining region 3 (CDR3) for the BCR sequence light chain.

17. CDR3.light.nt: the nucleotide sequence of complementarity determining region 3 (CDR3) for the BCR sequence light chain.

18. CDR3.light.nt: the nucleotide sequence of complementarity determining region 3 (CDR3) for the BCR sequence light chain.

19. CDR3.heavy.nt: the nucleotide sequence of complementarity determining region 3 (CDR3) for the BCR sequence heavy chain.

20. Species: the specie in which the TCR sequence is found (ig. Human, mice).

21. Valpha: identified V(variable) gene segment locus on alpha chain. The reference genes are derived from IMGT database.

22. Jalpha: the id of identified V(joining) gene segment locus on alpha chain. The reference genes are derived from IMGT database.

23. Vbeta: identified V(variable) gene segment for the sequence. The reference genes are derived from IMGT database.

24. Vbeta: identified V(variable) gene segment locus on beta chain. The reference genes are derived from IMGT database.

25. Dbeta: identified D(diversity) gene segment locus on beta chain. The reference genes are derived from IMGT database.

26. Jbeta: the id of identified V(joining) gene segment locus on beta chain. The reference genes are derived from IMGT database.

27. Seq.platform: the sequencing platform (eg. Sanger, ABI3100, ….).

28. Species: the species of samples.

29. Origin: the tissue from which the sample obtained.

30. Nucleotide.type: DNA or RNA, the material used for sequencing.

31. Cell_subtype: the cell type used for sequencing, CD8+ T cells, CD4+T cells or total T cells.

32. Prepare.method: the method used for librarying.

33. Evaluate.method: the assays are used for identifying the specificity of TCR to the antigen or disease.

34. Case.num: how many samples from patients are studied.

35. Control.type: the control sample used in the study.

36. Control.num: how many samples from control individuals are used in this study.

37. Filteration: the threshold for filting.

38. Journal: the journal on which the article published.

39. Pubmed_id: the id categorized by pubmed.

40. Grade: the reliability of specificity of the TCR sequence.

Evaluate.method and grade

There are four classes of methods been used to evaluate the specificity between sequences and antigens; These methods graded by their accuracy.

1. Selection of antigen-specific T cells using peptide-MHC multimers. peptide-MHC multimers are useful to identify the antigen-specific directly. If specificity of sequences in an article were evaluated by this method, 4 points will be given.

2. Antigen-specific ex vivo proliferation AND Antigen-specific stimulation ex vivo. They are classical methods, that stimulate cells ex vivo with antigen to proliferate them or just detect the proteins expressed by antigen-specific cells. 5 points.

3. Binding assay. These methods, containing SPR, ITC, MST and so on, are used to quantify the affinity between TCR/BCR and antigen. 4 points.

4. Laser microdissection. V/J specific antibodies are used to stain each type V and/or J motifs, then Laser microdissection is employed to detect them on tissue or cells. 1 point..

5. Statistical analysis. Actually, high frequency sequences or public clones are often considered as disease-specific clones. 2 points..

6. If more than two methods are employed, the points will be added up.

ICDnameDisease.nameCategoryAntigenAntigen.sequenceHLALocusCDR3.alpha.aaCDR3.beta.aaCDR3.alpha.ntCDR3.beta.ntValphaJalphaVbetaDbetaJbetaSeq.platformSpeciesOriginNucleotide.typeCell.subtypePrepare.methodEvaluate.methodCase.numControl.typeControl.numFilterationJournalPubmed.idGrade

ICDnameDisease.nameCategoryAntigenAntigen.sequenceHLALocusCDR3.gamma.aaCDR3.delta.aaCDR3.gamma.ntCDR3.delta.ntVgammaJgammaVdeltaDdeltaJdeltaSeq.platformSpeciesOriginNucleotide.typeCell.subtypePrepare.methodEvaluate.methodCase.numControl.typeControl.numFilterationJournalPubmed.idGrade

ICDnameDisease.nameCategoryAntigenAntigen.sequenceHLALocusCDR3.light.aaCDR3.heavy.aaCDR3.light.ntCDR3.heavy.ntVlightJlightVheavyDheavyJheavySeq.platformSpeciesOriginNucleotide.typeCell.subtypePrepare.methodEvaluate.methodCase.numControl.typeControl.numFilterationJournalPubmed.idGrade