Search results for "INFORMATICS"
showing 10 items of 2542 documents
Disentangling the complexity of low complexity proteins
2020
Abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichot…
Extracting similar sub-graphs across PPI Networks
2009
Singling out conserved modules (corresponding to connected sub-graphs) throughout protein-protein interaction networks of different organisms is a main issue in bioinformatics because of its potential applications in biology. This paper presents a method to discover highly matching sub-graphs in such networks. Sub-graph extraction is carried out by taking into account, on the one side, both protein sequence and network structure similarities and, on the other side, both quantitative and reliability information possibly available about interactions. The method is conceived as a generalization of a known technique, able to discover functional orthologs in interaction networks. Some preliminar…
Experimental Evaluation of Protein Secondary Structure Predictors
2009
Understanding protein biological function is a key issue in modern biology, which is largely determined by its 3D shape. Protein 3D shape, in its turn, is functionally implied by its amino acid sequence. Since the direct inspection of such 3D structures is rather expensive and time consuming, a number of software techniques have been developed in the last few years that predict a spatial model, either of the secondary or of the tertiary form, for a given target protein starting from its amino acid sequence. This paper offers a comparison of several available automatic secondary structure prediction tools. The comparison is of the experimental kind, where two relevant sets of proteins, a non…
Prediction of a Missing Protein Expression Map in the Context of the Human Proteome Project
2015
Experimental evidence for the entire human proteome has been defined in the Human Proteome Project, and it is publicly available in the neXtProt database. However, there are still human proteins for which reliable experimental evidence does not exist, and the identification of such information has become one of the overriding objectives in the chromosome-centric study of the human proteome. With this aim and considering the complexity of protein detection using shotgun and targeted proteomics, the research community has addressed the integration of transcriptomics and proteomics landscapes. Here, we describe an analytical pipeline that predicts the probability of a missing protein being exp…
Toward completion of the Earth’s proteome: an update a decade later
2017
Protein databases are steadily growing driven by the spread of new more efficient sequencing techniques. This growth is dominated by an increase in redundancy (homologous proteins with various degrees of sequence similarity) and by the incapability to process and curate sequence entries as fast as they are created. To understand these trends and aid bioinformatic resources that might be compromised by the increasing size of the protein sequence databases, we have created a less-redundant protein data set. In parallel, we analyzed the evolution of protein sequence databases in terms of size and redundancy. While the SwissProt database has decelerated its growth mostly because of a focus on i…
Assessing the low complexity of protein sequences via the low complexity triangle.
2020
Background Proteins with low complexity regions (LCRs) have atypical sequence and structural features. Their amino acid composition varies from the expected, determined proteome-wise, and they do not follow the rules of structural folding that prevail in globular regions. One way to characterize these regions is by assessing the repeatability of a sequence, that is, calculating the local propensity of a region to be part of a repeat. Results We combine two local measures of low complexity, repeatability (using the RES algorithm) and fraction of the most frequent amino acid, to evaluate different proteomes, datasets of protein regions with specific features, and individual cases of proteins…
Identification of Prostate-Enriched Proteins by In-depth Proteomic Analyses of Expressed Prostatic Secretions in Urine
2012
Urinary expressed prostatic secretion or "EPS-urine" is proximal tissue fluid that is collected after a digital rectal exam (DRE). EPS-urine is a rich source of prostate-derived proteins that can be used for biomarker discovery for prostate cancer (PCa) and other prostatic diseases. We previously conducted a comprehensive proteome analysis of direct expressed prostatic secretions (EPS). In the current study, we defined the proteome of EPS-urine employing Multidimensional Protein Identification Technology (MudPIT) and providing a comprehensive catalogue of this body fluid for future biomarker studies. We identified 1022 unique proteins in a heterogeneous cohort of 11 EPS-urines derived from …
Molecular modularity and asymmetry of the molluscan mantle revealed by a gene expression atlas
2018
15 pages; International audience; Background: Conchiferan molluscs construct a biocalcified shell that likely supported much of their evolutionary success.However, beyond broad proteomic and transcriptomic surveys of molluscan shells and the shell-forming mantle tissue,little is known of the spatial and ontogenetic regulation of shell fabrication. In addition, most efforts have been focused onspecies that deposit nacre, which is at odds with the majority of conchiferan species that fabricate shells using acrossed-lamellar microstructure, sensu lato. Results: By combining proteomic and transcriptomic sequencing with in situhybridization we have identified a suite of gene products associated …
Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative
2017
The Mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the iden…
Tools for Pathogen Proteomics: Fishing with Biomimetic Nanosponges
2017
The identification of the major virulence factors that drive pathogenicity is critical for gaining insight into the underlying molecular mechanisms of diseases. Although genetic approaches combined with functional analyses have markedly increased the rate of virulence factor discovery, the divergence between genome and proteome can impair the identification of important markers, in particular, of those that act in concert or depend on specific environmental factors. Recently, membrane-coated nanomaterials mimicking source cells of interest have emerged as powerful tools that can be used for improved tumor targeting and as "nanotraps" to capture chemokines and bacterial toxins. In this issue…