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PubMed1994

Access to DNA and protein databases on the Internet.

During the past year, the number of biological databases that can be queried via Internet has dramatically increased. This increase has resulted from the introduction of networking tools, such as Gopher and WAIS, that make it easy for research workers to index databases and make them available for on-line browsing. Biocomputing in the nineties will see the advent of more client/server options for the solution of problems in bioinformatics.

Amino Acid Sequence↗
PubMed2025

Prediction and Evaluation of Protein Aggregation with Computational Methods.

Protein and peptide aggregation has recently become one of the most studied biomedical problems due to its central role in several neurodegenerative disorders and of biotechnological importance. Multiple in silico methods, databases, tools, and algorithms have been developed to predict aggregation of proteins and peptides to better understand fundamental mechanisms of various aggregation diseases. Here, we attempt to provide a brief overview of bioinformatic methods and tools to better understand molecular mechanisms of aggregation disorders. Furthermore, through a better understanding of protein aggregation mechanisms, it might be possible to design novel therapeutic agents to treat and hopefully prevent protein aggregation diseases.

Computational Biology↗
PubMed2025

Investigating the molecular mechanisms, drug prediction, and validation of CCNA2 and MAD2L1 in esophageal squamous cell carcinoma based on bioinformatics.

OBJECTIVE: Aims to comprehensively investigate the expression patterns of CCNA2 and MAD2L1 in esophageal squamous cell carcinoma using bioinformatics methods. METHODS: Based on WGCNA analysis of gene mutation expression, methylation level distribution, mRNA expression and ESCC-related genes in public databases, were employed for investigating potential biomarkers for prognosis of esophageal squamous cell carcinoma(ESCC).Finally,. performing qRT-PCR and immunohistochemistry to validate. RESULTS: Ultimately identified 4 hub genes: CDK1, CCNA2,TOP2A and MAD2L1. Bioinformatics analysis showed high expression of these four genes in ESCC (P&#x2009;<&#x2009;0.05). CCNA2 and MAD2L1 were selected for subsequent analysis based on literature.3.Single gene enrichment analysis revealed significant enrichment of CCNA2 and MAD2L1 in pathways related to splicing, bladder cancer, non-homologous end joining and homologous recombination, glycosaminoglycan biosynthesis chondroitin sulfate, progesterone-mediated oocyte maturation and mismatch repair. PASTAA database indicated the involvement of transcription factors such as Roralpha1, Pou6f1, Roralpha2, Atf-1, Pax-3, C/ebpalpha, Nkx2-1 in the regulation of CCNA2, while no transcription factors were predicted for MAD2L1..Immune infiltration analysis revealed a close association between ESCC and plasma cells, CD8&#x2009;+&#x2009;T cells, monocytes, M0 macrophages, M1 macrophages, dendritic cells, and resting mast cells.Drug prediction for CCNA2 included 7 drugs such as ETHINYL ESTRADIOL, Seliciclib and TAMOXIFEN, while no drugs were predicted for MAD2L1.qRT-PCR and immunohistochemistry demonstrated high expression of CCNA2 in ESCC, while MAD2L1 showed no significant difference between ESCC and normal esophageal squamous epithelial tissues. CONCLUSION: CCNA2 and MAD2L1 may be potential biomarkers for ESCC, providing a novel basis for understanding the molecular mechanisms underlying ESCC pathogenesis.Additionally, the potential drugs predicted for CCNA2 may emerge as a new hope for ESCC patients in the future.

Humans↗
PubMed2004

Fractionation of peptides in proteomics with the use of pI-based approach and ZipTip pipette tips.

The aim of the work was to explore the utility of the in-solution isoelectric focusing (sIEF) fractionation method. That method was proved to be the alternative separation method of mixtures of protein tryptic digests in proteomics. Analysis of the identification of peptides was performed with the use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). For that research, previously designed the miniaturized multi-chamber fractionation sIEF device (75 microl volume for each chamber) based on polyacrylamide gel membranes with immobilines technology was utilized. To evaluate the efficiency and accuracy of sIEF fractionation combined with MS/MS peptides identification, bovine serum albumin (BSA) digest and mixture of five proteins digest were used. First, fractionation of bovine serum albumin digest sample was performed using sIEF method. Studies performed for that simple mixture of peptides proved the ability of the sIEF device to focus peptides mostly in one chamber. Additionally performed the correlation analysis between pI(calc) and pI(exp) values for identified peptides proved the possibility to obtain experimentally useful high correlation. That information was found to have a potential value for construction of additional constraint during false positives evaluation process among identified proteins. Next, studies on the sIEF fractionation were combined with the evaluation of practical use of ZipTip pipette tips to fractionate peptides in the case of simple mixture of proteins. For this, five proteins digest samples were used. The analysis without prior any fractionation enabled to identify very limited number of proteins. The significant improvement was obtained when one used sIEF alone or with combination with ZipTips fractionation prior to MS analysis. The proposed approach based on in-solution isoelectric focusing proved to be an efficient and accurate alternative fractionation method of protein digests and can be considered as the first useful dimension in two-dimensional proteomics separations. Moreover, analytical information from that pI-based fractionation method can be considered as the additional source of database matching constraint. It can also be a valuable tool for analytical and bioinformatic studies of peptides fractionation in proteomics.

Amino Acid Sequence↗
PubMed2006

Characterization of the human salivary proteome by capillary isoelectric focusing/nanoreversed-phase liquid chromatography coupled with ESI-tandem MS.

Saliva is a readily available body fluid with great diagnostic potential. The foundation for saliva-based diagnostics, however, is the development of a complete catalog of secreted and "leaked" proteins detectable in saliva. By employing a capillary isoelectric focusing-based multidimensional separation platform coupled with electrospray ionization tandem mass spectrometry (MS), a total of 5338 distinct peptides were sequenced, leading to the identification of 1381 distinct proteins. A search of bacterial protein sequences also identified many peptides unique to several organisms and unique to the NCBI nonredundant database. To the best of our knowledge, this proteome study represents the largest catalog of proteins measured from a single saliva sample to date. Data analysis was performed on individual MS/MS spectra using the highly specific peptide identification algorithm, OMSSA. Searches were conducted against a decoyed SwissProt human database to control the false-positive rate at 1%. Furthermore, the well-curated SwissProt sequences represent perhaps the least redundant human protein sequence database (12,484 records versus the 50,009 records found in the International Protein Index human database), therefore minimizing multiple protein inferences from single peptides. This combined bioanalytical and bioinformatic approach has established a solid foundation for building up the human salivary proteome for the realization of the diagnostic potential of saliva.

Chromatography, Liquid↗
PubMed2006

The WWWH of remote homolog detection: the state of the art.

The detection of remote homolog pairs of proteins using computational methods is a pivotal problem in structural bioinformatics, aiming to compute protein folds on the basis of information in the database of known structures. In the last 25 years, several methods have been developed to tackle this problem, based on different approaches including sequence-sequence alignments and/or structure comparison. In this article, we will briefly discuss When, Why, Where and How (WWWH) to perform remote homology search, reviewing some of the most widely adopted computational approaches. The specific aim is highlighting the basic criteria implemented by different research groups and commenting on the status of the art as well as on still-open questions.

Algorithms↗
PubMed2004

Systematic recovery and analysis of full-ORF human cDNA clones.

The Mammalian Gene Collection (MGC) consortium (http://mgc.nci.nih.gov) seeks to establish publicly available collections of full-ORF cDNAs for several organisms of significance to biomedical research, including human. To date over 15,200 human cDNA clones containing full-length open reading frames (ORFs) have been identified via systematic expressed sequence tag (EST) analysis of a diverse set of cDNA libraries; however, further systematic EST analysis is no longer an efficient method for identifying new cDNAs. As part of our involvement in the MGC program, we have developed a scalable method for targeted recovery of cDNA clones to facilitate recovery of genes absent from the MGC collection. First, cDNA is synthesized from various RNAs, followed by polymerase chain reaction (PCR) amplification of transcripts in 96-well plates using gene-specific primer pairs flanking the ORFs. Amplicons are cloned into a sequencing vector, and full-length sequences are obtained. Sequences are processed and assembled using Phred and Phrap, and analyzed using Consed and a number of bioinformatics methods we have developed. Sequences are compared with the Reference Sequence (RefSeq) database, and validation of sequence discrepancies is attempted using other sequence databases including dbEST and dbSNP. Clones with identical sequence to RefSeq or containing only validated changes will become part of the MGC human gene collection. Clones containing novel splice variants or polymorphisms have also been identified. Our approach to clone recovery, applied at large scale, has the potential to recover many and possibly most of the genes absent from the MGC collection.

Cloning, Molecular↗
PubMed2005

A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools.

BACKGROUND: This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium (MPP+) in a rat adrenal pheochromocytoma cell line (PC12 cells) using bioinformatics tools. MPP+ depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP+-induced neurotoxicity is still unclear. RESULTS: In this study, Agilent rat oligo 22K microarrays were used to examine alterations in gene expression of PC12 cells after 500 muM MPP+ treatment. Relative gene expression of control and treated cells represented by spot intensities on the array chips was analyzed using bioinformatics tools. Raw data from each array were input into the NCTR ArrayTrack database, and normalized using a Lowess normalization method. Data quality was monitored in ArrayTrack. The means of the averaged log ratio of the paired samples were used to identify the fold changes of gene expression in PC12 cells after MPP+ treatment. Our data showed that 106 genes and ESTs (Expressed Sequence Tags) were changed 2-fold and above with MPP+ treatment; among these, 75 genes had gene symbols and 59 genes had known functions according to the Agilent gene Refguide and ArrayTrack-linked gene library. The mechanism of MPP+-induced toxicity in PC12 cells was analyzed based on their genes functions, biological process, pathways and previous published literatures. CONCLUSION: Multiple pathways were suggested to be involved in the mechanism of MPP+-induced toxicity, including oxidative stress, DNA and protein damage, cell cycling arrest, and apoptosis.

1-Methyl-4-phenylpyridinium↗
PubMed2002

Computational discovery of sense-antisense transcription in the human and mouse genomes.

BACKGROUND: Overlapping but oppositely oriented transcripts have the potential to form sense-antisense perfect double-stranded (ds) RNA duplexes. Over recent years, the number and variety of examples of mammalian gene-regulatory phenomena in which endogenous dsRNA duplexes have been proposed or demonstrated to participate has greatly increased. These include genomic imprinting, RNA interference, translational regulation, alternative splicing, X-inactivation and RNA editing. We computationally mined public mouse and human expressed sequence tag (EST) databases to search for additional examples of bidirectionally transcribed genomic regions. RESULTS: Our bioinformatics approach identified over 217 candidate overlapping transcriptional units, almost all of which are novel. From experimental validation of a subset of our predictions by orientation-specific RT-PCR, we estimate that our methodology has a specificity of 84% or greater. In many cases, regions of sense-antisense overlap within the 5'- or 3'-untranslated regions of a given transcript correlate with genomic patterns of mouse-human conservation. CONCLUSIONS: Our results, in conjunction with the literature, bring the total number of predicted and validated examples of overlapping but oppositely oriented transcripts to over 300. Several of these cases support the hypothesis that a subset of the instances of substantial mouse-human conservation in the 5' and 3' UTRs of transcripts might be explained in part by functionality of an overlapping transcriptional unit.

Alternative Splicing↗
PubMed2002

The promise of structural genomics in the discovery of new antimicrobial agents.

Structural Genomics stands out among the emerging fields of proteomics since it influences the drug discovery process at so many points. Recent developments in protein expression technologies, x-ray crystallography and NMR spectroscopy provide the essential elements for high-throughput structure determination platforms. Bioinformatics methods to interrogate the resulting data will provide comprehensive, genome-wide databases of protein structure. Genomic sequencing and methods for high-throughput expression and protein purification are furthest advanced for microbial genes and so these have been the early targets for structural genomics initiatives. The information will be invaluable in understanding gene function, designing broad-spectrum small molecule inhibitors and in better understanding drug-host interactions.

Anti-Bacterial Agents↗
PubMed2022

An Exosomal miRNA Biomarker for the Detection of Pancreatic Ductal Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) remains a difficult tumor to diagnose and treat. To date, PDAC lacks routine screening with no markers available for early detection. Exosomes are 40-150 nm-sized extracellular vesicles that contain DNA, RNA, and proteins. These exosomes are released by all cell types into circulation and thus can be harvested from patient body fluids, thereby facilitating a non-invasive method for PDAC detection. A bioinformatics analysis was conducted utilizing publicly available miRNA pancreatic cancer expression and genome databases. Through this analysis, we identified 18 miRNA with strong potential for PDAC detection. From this analysis, 10 (MIR31, MIR93, MIR133A1, MIR210, MIR330, MIR339, MIR425, MIR429, MIR1208, and MIR3620) were chosen due to high copy number variation as well as their potential to differentiate patients with chronic pancreatitis, neoplasms, and PDAC. These 10 were examined for their mature miRNA expression patterns, giving rise to 18 mature miRs for further analysis. Exosomal RNA from cell culture media was analyzed via RTqPCR and seven mature miRs exhibited statistical significance (miR-31-5p, miR-31-3p, miR-210-3p, miR-339-5p, miR-425-5p, miR-425-3p, and miR-429). These identified biomarkers can potentially be used for early detection of PDAC.

Humans↗
PubMed2003

[Analysis of p53 mutational spectra of esophageal squamous cell carcinomas from Linzhou, comparison with esophageal and other cancers from other areas].

OBJECTIVE: To study the etiological clues involved (in esophageal cancer in Linzhou, Henan, a high-incidence area for esophageal cancer) by analyzing p53 mutational spectrum from esophageal precancerous and cancerous lesions. METHODS: Using bolt bioinformatic and Monte Carlo methods to analyze p53 mutation spectra from "The IARC Database of Somatic p53 Mutations in Human Tumors and Cell Lines", "p53 Database at Institute Curic" and to establish a local database based on these data using the FileMark Pro 3.0 software to allow fast and off-line analysis on a PC from the authors' laboratory. RESULTS: We found that esophageal squamous cell carcinomas from Linzhou had a lower prevalence of base substitutions associated with strand bias than those from other areas (32.8% vs 39.8%). However, a higher prevalence of G:C-->A:T transitions at CpG site (29.6% vs16.4%) was found. Esophageal squamous cell carcinomas from Linzhou displayed a distinctive profile of mutation hotspots, including codons 273 (covers 11.3% of all missense mutations), 175 (9.7%), 158 (9.7%), 159 (6.5%) and 282 (6.5%), all of which were at the CpG site. Statistical analysis showed that the p53 mutation profiles between esophageal squamous cell carcinomas from Linzhou and those from other areas were different (P = 0.02). The p53 mutation profiles of esophageal squamous cell carcinomas from Linzhou and from other areas were also different from cancer of the head and neck. CONCLUSION: Data showed that the p53 mutational spectrum of esophageal squamous cell carcinomas from Linzhou baring the characteristics of those caused both by endogenous and exogenous mutagenic agents, suggesting the potential involvement of chronic inflammation, unique dietary habits and carcinogen exposure in the pathogenesis of esophageal squamous cell carcinoma in Linzhou.

Carcinogens, Environmental↗
PubMed2005

Genomic resources for chicken.

The recent sequencing and draft assembly of a chicken genome has provided biologists with an invaluable research tool that complements a growing list of additional avian genomic resources. For many researchers, finding and using these resources is challenging, because information is presented through an increasing number of Web sites and browser navigation frequently requires specific knowledge and expertise. This primer provides an overview of online genomic resources for the chicken, including the Ensembl, UCSC, and NCBI annotated chicken genome browsers; expressed sequence tag and in situ hybridization databases; and sources for microarrays, cDNAs, and bacterial artificial chromosomes (BACs). Several short tutorials oriented toward the biologist with limited bioinformatics skills outline how to retrieve several types of commonly needed information and reagents.

Animals↗
PubMed2006

Analysis of molecular recognition features (MoRFs).

Several proteomic studies in the last decade revealed that many proteins are either completely disordered or possess long structurally flexible regions. Many such regions were shown to be of functional importance, often allowing a protein to interact with a large number of diverse partners. Parallel to these findings, during the last five years structural bioinformatics has produced an explosion of results regarding protein-protein interactions and their importance for cell signaling. We studied the occurrence of relatively short (10-70 residues), loosely structured protein regions within longer, largely disordered sequences that were characterized as bound to larger proteins. We call these regions molecular recognition features (MoRFs, also known as molecular recognition elements, MoREs). Interestingly, upon binding to their partner(s), MoRFs undergo disorder-to-order transitions. Thus, in our interpretation, MoRFs represent a class of disordered region that exhibits molecular recognition and binding functions. This work extends previous research showing the importance of flexibility and disorder for molecular recognition. We describe the development of a database of MoRFs derived from the RCSB Protein Data Bank and present preliminary results of bioinformatics analyses of these sequences. Based on the structure adopted upon binding, at least three basic types of MoRFs are found: alpha-MoRFs, beta-MoRFs, and iota-MoRFs, which form alpha-helices, beta-strands, and irregular secondary structure when bound, respectively. Our data suggest that functionally significant residual structure can exist in MoRF regions prior to the actual binding event. The contribution of intrinsic protein disorder to the nature and function of MoRFs has also been addressed. The results of this study will advance the understanding of protein-protein interactions and help towards the future development of useful protein-protein binding site predictors.

Algorithms↗
PubMed2005

Bioinformatic "Harvester": a search engine for genome-wide human, mouse, and rat protein resources.

Harvester is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. The Harvester search engine works similar to Google, offering genome-wide ranked results at very high speed. Here we describe how to use this bioinformatic tool along with selected examples.

Animals↗
PubMed2001

Protein--protein interaction maps: a lead towards cellular functions.

The availability of complete genome sequences now permits the development of tools for functional biology on a proteomic scale. Several experimental approaches or in silico algorithms aim at clustering proteins into networks with biological significance. Among those, the yeast two-hybrid system is the technology of choice to detect protein-protein interactions. Recently, optimized versions were applied at a genomic scale, leading to databases on the web. However, as with any other 'genetic' assay, yeast two-hybrid assays are prone to false positives and false negatives. Here we discuss these various technologies, their general limitations and the potential advances they make possible, especially when in combination with other functional genomics or bioinformatics analyses.

Animals↗
PubMed2006

Classification of protein quaternary structure by functional domain composition.

BACKGROUND: The number and the arrangement of subunits that form a protein are referred to as quaternary structure. Quaternary structure is an important protein attribute that is closely related to its function. Proteins with quaternary structure are called oligomeric proteins. Oligomeric proteins are involved in various biological processes, such as metabolism, signal transduction, and chromosome replication. Thus, it is highly desirable to develop some computational methods to automatically classify the quaternary structure of proteins from their sequences. RESULTS: To explore this problem, we adopted an approach based on the functional domain composition of proteins. Every protein was represented by a vector calculated from the domains in the PFAM database. The nearest neighbor algorithm (NNA) was used for classifying the quaternary structure of proteins from this information. The jackknife cross-validation test was performed on the non-redundant protein dataset in which the sequence identity was less than 25%. The overall success rate obtained is 75.17%. Additionally, to demonstrate the effectiveness of this method, we predicted the proteins in an independent dataset and achieved an overall success rate of 84.11% CONCLUSION: Compared with the amino acid composition method and Blast, the results indicate that the domain composition approach may be a more effective and promising high-throughput method in dealing with this complicated problem in bioinformatics.

Algorithms↗