Advances in Experimental Medicine and Biology
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Bioinformatics tools for proteomics data interpretation
amino acid, 65072-01-7; protein, 67254-75-5; Biomarkers; Multiprotein Complexes; Proteins; Proteome
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. © Springer International Publishing Switzerland 2016.
BioGRID; DAVID; Gene ontology; HPRD; IntAct; Interactome mapping; IPA; KEGG; MINT; MPIDB; PANTHER; PIPs; Proteomics data interpretation; STRING; TAIR amino acid; biological marker; biological marker; multiprotein complex; protein; proteome; BioGRID database; bioinformatics; classification; data analysis software; DAVID; DNA microarray; DNA sequence; gene list analysis; gene ontology; GeneCards database; genetic database; Human Protein Reference Database; IntAct database; KEGG database; metagenome; Microbial Protein Interaction Database; MINT database; next generation sequencing; nucleotide sequence; PANTHER classification; pathway maps analysis; priority journal; protein database; protein expression; protein processing; protein protein database; proteomics; STRING database; TAIR database; algorithm; animal; biology; data mining; genetics; high throughput screening; human; mass spectrometry; procedures; protein analysis; protein database; protein protein interaction; proteomics; reproducibility; search engine; software; web browser; Algorithms; Animals; Biomarkers; Computational Biology; Data Mining; Databases, Protein; High-Throughput Screening Assays; Humans; Mass Spectrometry; Multiprotein Complexes; Protein Interaction Mapping; Protein Interaction Maps; Protein Processing, Post-Translational; Proteins; Proteome; Proteomics; Reproducibility of Results; Search Engine; Software; Web Browser
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Instituto de Ciencia y Tecnología del Distrito Federal, ICyTDF
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