Research Article

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Computational biology; Gene expression profiling; Humans; Models, Statistical; Reproducibility of Results

Microarray gene expression technology provides a systematic approach to patient classification. However, microarray data pose a great computational challenge owing to their large dimensionality, small sample sizes, and potential correlations among genes. A recent study has shown that gene-gene correlations have a positive effect on the accuracy of classification models, in contrast to some ... more

M. Pan; J. Zhang
Bacteria; Bacterial Proteins; Computational biology; Databases, Protein; Gene Ontology; Humans; Protein Interaction Mapping

Since the first assembled genomes, gene sequences alone have not been sufficient to understand complex metabolic processes involving several genes, each playing distinct roles. To identify their roles, a network of interactions, wherein each gene is a node, should be created. Edges connecting nodes are evidence of interaction, for instance, of gene products coexisting in the same cellular ... more

G.S. Oliveira; A.R. Santos
Algorithms; Amino acid sequence; Amino acids; Animals; binding sites; Computational biology; Databases, Protein; Humans; Hydrophobic and Hydrophilic Interactions; Models, Theoretical; Neural Networks, Computer; Phosphorylation; Proteins; Reproducibility of Results; Support vector machine

Phosphorylation is an important part of post-translational modifications of proteins, and is essential for many biological activities. Phosphorylation and dephosphorylation can regulate signal transduction, gene expression, and cell cycle regulation in many cellular processes. Phosphorylation is extremely important for both basic research and drug discovery to rapidly and correctly identify ... more

R.Z. Han; D. Wang; Y.H. Chen; L.K. Dong; Y.L. Fan
Amino acid sequence; Base Sequence; Computational biology; Databases, Genetic; Humans; Models, Molecular; Open Reading Frames; Precision Medicine; Proteins; Sequence alignment; Sequence Analysis, DNA

Technological advancements in recent years have promoted a marked progress in understanding the genetic basis of phenotypes. In line with these advances, genomics has changed the paradigm of biological questions in full genome-wide scale (genome-wide), revealing an explosion of data and opening up many possibilities. On the other hand, the vast amount of information that has been generated ... more

W.J.S. Diniz; F. Canduri
Arthritis, Rheumatoid; Gene expression profiling; Humans; Models, Genetic; Monte Carlo method; Signal transduction; Transcriptome

We attempted to identify significant pathway cross-talk in rheumatoid arthritis (RA) by the Monte Carlo cross-validation (MCCV) method. We therefore obtained and preprocessed the gene expression profile of RA. MCCV involves identifying differentially expressed genes (DEGs), identifying differential pathways (DPs), calculating the discriminating score (DS) of the pathway cross-talk, and random ... more

W. Song; Y.M. Zhang; T. Ma; J. Wang; K.Z. Wang
Computational biology; Distributed systems; Interpro; Tools

Interpro is a widely used tool for protein annotation in genome sequencing projects, demanding a large amount of computation and representing a huge time-consuming step. We present a strategy to execute programs using databases Pfam, PROSITE and ProDom of Interpro in a distributed environment using a Java-based messaging system. We developed a two-layer scheduling architecture of the ... more

Ede O. Ribeiro; G.G. Zerlotini; I.R.M. Lopes; V.B.R. Ribeiro; A.C.M. Melo; M.Emilia M.T. Walter; M.Emilia M.T. Walter; M.Mota Costa; B.I.O.F.O.C.O. Network
Apoptosis; bcl-X Protein; Cell Line, Tumor; Cell proliferation; Cell survival; Female; Gene Expression Regulation, Neoplastic; Humans; MicroRNAs; Uterine cervical neoplasms

Cervical cancer is a life-threatening condition. MicroRNAs (miRNAs) can promote or inhibit cell death and proliferation. The present study investigated the effect of miRNA 421 on the growth and apoptosis of cervical cancer cells. miRNA 421 and control miRNA were synthesized and transfected into c-33a cervical cancer cells. A thiazolyl blue tetrazolium bromide assay, caspase-3 activity, and ... more

X.J. Lai; X.Y. Cheng; L.D. Hu
2016 Dec 02
Asians; Child; Chromosome Deletion; Chromosomes, Human, Pair 2; Fingers; Heart Defects, Congenital; Hedgehog Proteins; Humans; Karyotype; male; Syndactyly; Waardenburg Syndrome

Reports of terminal and interstitial deletions of the long arm of chromosome 2 are rare in the literature. Here, we present a case report concerning a Chinese boy with a 47,XYY karyotype and a de novo deletion comprising approximately 5 Mb between 2q35 and q36.1, along with syndactyly, type III Waardenburg syndrome, and congenital heart disease. High-resolution chromosome analysis to detect ... more

D. Wang; G.F. Ren; H.Z. Zhang; C.Y. Yi; Z.J. Peng
2016 Dec 02
Adult; Alanine; Arginine; Asians; Diabetes Mellitus, Type 2; Female; Genetic predisposition to disease; Genotype; Glutamine; Humans; Leucine; male; Middle Aged; Polymorphism, Single Nucleotide; Regression Analysis; Superoxide dismutase; Threonine

The most common type of endocrine disease is type 2 diabetes mellitus (T2DM); genetic factors contribute to the development to T2DM. In this study, we investigated the role of the Leu53Leu, Arg213Gly, and Ala40Thr polymorphisms in extracellular superoxide dismutase (EC-SOD) gene in the development of T2DM in a Chinese population. DNA was extracted from peripheral blood samples obtained from ... more

Y.M. Yang; X.R. Xie; A.L. Jin
Cell Hypoxia; Cell Movement; Cell proliferation; Epithelial-mesenchymal transition; Gene Expression Regulation, Neoplastic; HCT116 Cells; Humans; Hypoxia-Inducible Factor 1, alpha Subunit; Rectal Neoplasms; Snail Family Transcription Factors

Rectal cancer is a commonly observed tumor in clinics, and epithelial-mesenchymal transition (EMT) is very important for tumor invasion and metastasis. We established a rectal cancer HCT-116 cell hypoxia model and detected cell proliferation, invasion, and EMT-related protein expression in this model, aiming to analyze the effect of hypoxia on rectal cancer cell EMT. Rectal cancer cell line ... more

L.L. Sun; Z. Song; W.Z. Li; S.Y. Tang