Bioinformatics Tools for Proteomics Data Interpretation
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 developm
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Karla Grisel Caldero´n-Gonza´lez, Jesu´s Herna´ndez-Monge, Marı´a Esther Herrera-Aguirre, and Juan Pedro Luna-Arias
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. K.G. Caldero´n-Gonza´lez • M.E. Herrera-Aguirre J.P. Luna-Arias (*) Departamento de Biologı´a Celular, Centro de Investigacio´n y de Estudios Avanzados del Instituto Polite´cnico Nacional (Cinvestav-IPN), Av. Instituto Polite´cnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360 Ciudad de Me´xico, Mexico e-mail: [email protected]; [email protected]; [email protected]
J. Herna´ndez-Monge Instituto de Fı´sica, Universidad Auto´noma de San Luis Potosı´, Av. Manuel Nava 6, Zona Universitaria, C.P. 78290 San Luis Potosı´, S.L.P., Mexico
# Springer International Publishing Switzerland 2016 H. Mirzaei and M. Carrasco (eds.), Modern Proteomics – Sample Preparation, Analysis and Practical Applications, Advances in Experimental Medicine and Biology 919, DOI 10.1007/978-3-319-41448-5_16
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Keywords
Proteomics data interpretation • Interactome mapping • Gene Ontology • STRING • MINT • IntAct • HPRD • BioGRID • PIPs • MPIDB • TAIR • PANTHER • DAVID • KEGG • IPA
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 [1]. The development of highthroughput 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
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