Immunoinformatics and systems biology in personalized medicine.

Every year new databases and tools for the storage and analysis of biological data are developed, updated, and discontinued. For this reason it is very important to have a clear picture of the major repositories providing information about the availability of these databases and tools as well as a brief description of them. This chapter provides an overview of the most important information sources which can guide researchers through the process of selecting databases and tools of interest for immunoinformatics and systems biology in personalized medicine. As an example of a particular resource of interest that combines a curated database and tools for data analysis, this chapter also includes a description of InnateDB. This database offers access to curated information relative to the innate immune response in a systems biology context.

[1]  Gary D Bader,et al.  NetPath: a public resource of curated signal transduction pathways , 2010, Genome Biology.

[2]  Yu Zhang,et al.  HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma , 2005, Nucleic Acids Res..

[3]  Joo Chuan Tong,et al.  MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures , 2011, Bioinform..

[4]  Matthew R. Laird,et al.  Protein Protein Interaction Network Evaluation for Identifying Potential Drug Targets , 2009 .

[5]  Nigel W. Hardy,et al.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.

[6]  Philip E. Bourne,et al.  IEDB-3D: structural data within the immune epitope database , 2010, Nucleic Acids Res..

[7]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[8]  Gajendra P. S. Raghava,et al.  AntigenDB: an immunoinformatics database of pathogen antigens , 2009, Nucleic Acids Res..

[9]  Channa K. Hattotuwagama,et al.  AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data , 2005, Immunome research.

[10]  Yongqun He,et al.  Protegen: a web-based protective antigen database and analysis system , 2010, Nucleic Acids Res..

[11]  Anna Tramontano,et al.  A database of immunoglobulins with integrated tools: DIGIT , 2011, Nucleic Acids Res..

[12]  Gajendra P. S. Raghava,et al.  MHCBN: a comprehensive database of MHC binding and non-binding peptides , 2003, Bioinform..

[13]  Wonyong Kim,et al.  Development of a 16S-23S rRNA intergenic spacer-based quantitative PCR assay for improved detection and enumeration of Lactococcus garvieae. , 2013, FEMS microbiology letters.

[14]  Kenneth H. Buetow,et al.  PID: the Pathway Interaction Database , 2008, Nucleic Acids Res..

[15]  Avner Schlessinger,et al.  Epitome: database of structure-inferred antigenic epitopes , 2005, Nucleic Acids Res..

[16]  Michael Zouberakis,et al.  MUGEN mouse database; Animal models of human immunological diseases , 2007, Nucleic Acids Res..

[17]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[18]  C. Schönbach,et al.  An Update on the Functional Molecular Immunology (FIMM) Database , 2005, Applied bioinformatics.

[19]  Ellis L. Reinherz,et al.  PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands , 2005, Nucleic Acids Res..

[20]  Rekha Gupta,et al.  DyNAVacS: an integrative tool for optimized DNA vaccine design , 2006, Nucleic Acids Res..

[21]  Patrice Duroux,et al.  IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences , 2005, Nucleic Acids Res..

[22]  James Robinson,et al.  IPD—the Immuno Polymorphism Database , 2004, Nucleic acids research.

[23]  Jong C. Park,et al.  DigSee: disease gene search engine with evidence sentences (version cancer) , 2013, Nucleic Acids Res..

[24]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[25]  K. Schwarz,et al.  IL2RGbase: a database of γc-chain defects causing human X-SCID , 1996 .

[26]  Sylvia Janetzki,et al.  Advancing the field of cancer immunotherapy , 2012, Oncoimmunology.

[27]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[28]  James Robinson,et al.  The IMGT/HLA database , 2008, Nucleic Acids Res..

[29]  E. Jaffe,et al.  Natural history of autoimmune lymphoproliferative syndrome associated with FAS gene mutations. , 2014, Blood.

[30]  Gajendra P.S. Raghava,et al.  Searching and mapping of B-cell epitopes in Bcipep database. , 2007, Methods in molecular biology.

[31]  L A Segel,et al.  Controlling the immune system: diffuse feedback via a diffuse informational network. , 2001, Novartis Foundation symposium.

[32]  J. Minei,et al.  Examination with next-generation sequencing technology of the bacterial microbiota in bronchoalveolar lavage samples after traumatic injury. , 2013, Surgical infections.

[33]  Ida Retter,et al.  VBASE2, an integrative V gene database , 2004, Nucleic Acids Res..

[34]  Philip E. Bourne,et al.  Immune epitope database analysis resource , 2012, Nucleic Acids Res..

[35]  Alan Aderem,et al.  Immunology in the post-genomic era , 2001, Nature Immunology.

[36]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[37]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[38]  Kristian Rother,et al.  SuperHapten: a comprehensive database for small immunogenic compounds , 2006, Nucleic Acids Res..

[39]  David S. Goodsell,et al.  The RCSB Protein Data Bank: new resources for research and education , 2012, Nucleic Acids Res..

[40]  Ronald C. Taylor,et al.  Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). , 2006, Omics : a journal of integrative biology.

[41]  Feng Liu,et al.  The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge , 2007, Nucleic Acids Res..

[42]  S. Desmond-Hellmann Toward Precision Medicine: A New Social Contract? , 2012, Science Translational Medicine.

[43]  Marie-Paule Lefranc,et al.  IMGT , the international ImMunoGeneTics information system , 2003 .

[44]  Alessandro Sette,et al.  Query enhancement through the practical application of ontology: the IEDB and OBI , 2013, J. Biomed. Semant..

[45]  Alessandro Sette,et al.  The Immune Epitope Database 2.0 , 2009, Nucleic Acids Res..

[46]  Rocío Romero-Záliz,et al.  PGMRA: a web server for (phenotype × genotype) many-to-many relation analysis in GWAS , 2013, Nucleic Acids Res..

[47]  Maria Keays,et al.  ArrayExpress update—trends in database growth and links to data analysis tools , 2012, Nucleic Acids Res..