Search results for " mining"

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…

A computer system to perform structure comparison using TOPS representations of protein structure

2001

We describe the design and implementation of a fast topology-based method for protein structure comparison. The approach uses the TOPS topological representation of protein structure, aligning two structures using a common discovered pattern and generating measure of distance derived from an insert score. Heavy use is made of a constraint-based pattern-matching algorithm for TOPS diagrams that we have designed and described elsewhere (Bioinformatics 15(4) (1999) 317). The comparison system is maintained at the European Bioinformatics Institute and is available over the Web at tops.ebi.ac.uk/tops. Users submit a structure description in Protein Data Bank (PDB) format and can compare it with …

RPPanalyzer Toolbox: An improved R package for analysis of reverse phase protein array data

2014

Analysis of large-scale proteomic data sets requires specialized software tools, tailored toward the requirements of individual approaches. Here we introduce an extension of an open-source software solution for analyzing reverse phase protein array (RPPA) data. The R package RPPanalyzer was designed for data preprocessing followed by basic statistical analyses and proteomic data visualization. In this update, we merged relevant data preprocessing steps into a single user-friendly function and included a new method for background noise correction as well as new methods for noise estimation and averaging of replicates to transform data in such a way that they can be used as input for a new t…

Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data

2013

Background The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. Technologies like mass spectrometry are commonly being used in proteomic research. Mass spectrometry signals show the proteomic profiles of the individuals under study at a given time. These profiles correspond to the recording of a large number of proteins, much larger than the number of individuals. These variables come in addition to or to complete classical clinical variables. The objective of this study is to evaluate and compare the predictive ability of new and existing models combining mass spectrometry data and classical clinical variables. This study was co…

General Statistical Framework for Quantitative Proteomics by Stable Isotope Labeling

2014

Pedro J. Navarro et al.

Understanding the clinical behavior of relapsed colon cancers with microsatellite instability relative to BRAF mutations

2019

Background Microsatellite instable/deficient mismatch repair (MSI/dMMR) metastatic colorectal cancers have been reported to have a poor prognosis. Frequent co-occurrence of MSI/dMMR and BRAFV600E complicates the association. Patients and methods Patients with resected stage III colon cancer (CC) from seven adjuvant studies with available data for disease recurrence and MMR and BRAFV600E status were analyzed. The primary end point was survival after recurrence (SAR). Associations of markers with SAR were analyzed using Cox proportional hazards models adjusted for age, gender, performance status, T stage, N stage, primary tumor location, grade, KRAS status, and timing of recurrence. Results A…

How to Write a Research Protocol: Tips and Tricks

2018

There is a need to reassess the most appropriate indications for stress echocardiography in the current era, in patients with suspect or known coronary artery disease (CAD), and also the most helpful additional parameters that can be easily calculated in clinical practice to increase the known suboptimal sensitivity for obstructive CAD of this test. The current review tries to clarify what is and what should be the proper role for functional testing in general, but specifically regarding modern stress echocardiography in the current practice, for suspected CAD and/or atypical chest pain. Few candidate additional parameters beyond wall motion assessment are here suggested to improve diagnost…

Treatment of patients with spinal muscular atrophy 5q: Towards a new protocol.

2021

The diagnostic protocol of congenital uterine anomalies

2008

Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches.

2015

Proton transfer reactions are of crucial interest for the investigation of proteins. We have investigated the accuracy of commonly used quantum chemical methods for the description of proton transfer reactions in different environments (gas phase, COSMO, QM/MM) using the proton transfer between the catalytic dyad residues cysteine 145 and histidine 41 of SARS coronavirus main protease as a case study. The test includes thermodynamic, kinetic, and structural properties. The study comprises computationally demanding ab initio approaches (HF, CC2, MP2, SCS-CC2, SCS-MP2, CCSD(T)), popular density functional theories (BLYP, B3LYP, M06-2X), and semiempirical methods (MNDO/d, AM1, RM1, PM3, PM6). …