title: Bioinformatics Tools for Proteomics Data Interpretation.
abstract: Biological systems function via intricate cellular processes and networks in which RNAs, metabolites, proteins and other cellular compounds have a precise role and are exquisitely regulated (Kumar and Mann, FEBS Lett 583(11):1703-1712, 2009). The development of high-throughput technologies, such as the Next Generation DNA Sequencing (NGS) and DNA microarrays for sequencing genomes or metagenomes, have triggered a dramatic increase in the last few years in the amount of information stored in the GenBank and UniProt Knowledgebase (UniProtKB). GenBank release 210, reported in October 2015, contains 202,237,081,559 nucleotides corresponding to 188,372,017 sequences, whilst there are only 1,222,635,267,498 nucleotides corresponding to 309,198,943 sequences from Whole Genome Shotgun (WGS) projects. In the case of UniProKB/Swiss-Prot, release 2015_12 (December 9, 2015) contains 196,219,159 amino acids that correspond to 550,116 entries. Meanwhile, UniProtKB/TrEMBL (release 2015_12 of December 9 2015) contains 1,838,851,8871 amino acids corresponding to 555,270,679 entries. Proteomics has also improved our knowledge of proteins that are being expressed in cells at a certain time of the cell cycle. It has also allowed the identification of molecules forming part of multiprotein complexes and an increasing number of posttranslational modifications (PTMs) that are present in proteins, as well as the variants of proteins expressed.
authors.affiliation: Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, Ciudad de México, Mexico.
authors.forename: Karla Grisel
authors.initials: KG
authors.lastname: Calderón-González
authors.affiliation: Instituto de Física, Universidad Autónoma de San Luis Potosí, Av. Manuel Nava 6, Zona Universitaria, C.P. 78290, San Luis Potosí, S.L.P., Mexico.
authors.forename: Jesús
authors.initials: J
authors.lastname: Hernández-Monge
authors.affiliation: Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, Ciudad de México, Mexico.
authors.forename: María Esther
authors.initials: ME
authors.lastname: Herrera-Aguirre
authors.affiliation: Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, Ciudad de México, Mexico. jpluna@cell.cinvestav.mx.
authors.forename: Juan Pedro
authors.initials: JP
authors.lastname: Luna-Arias
mesh_terms: D000465:Algorithms; D000818:Animals; D015415:Biomarkers / Q000032:analysis; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D057166:High-Throughput Screening Assays; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D046912:Multiprotein Complexes; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis* / Q000235:genetics; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D057386:Search Engine; D012984:Software; D064878:Web Browser
chemical_list: D015415:Biomarkers; D046912:Multiprotein Complexes; D011506:Proteins; D020543:Proteome
keywords: BioGRID; DAVID; Gene Ontology; HPRD; IPA; IntAct; Interactome mapping; KEGG; MINT; MPIDB; PANTHER; PIPs; Proteomics data interpretation; STRING; TAIR