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PubMed2004

Formalization of mouse embryo anatomy.

MOTIVATION: The Edinburgh Mouse Atlas and Gene Expression Database project has developed a digital atlas of mouse development to provide a spatio-temporal framework for spatially mapped data such as in situ gene expression and cell lineage. As part of this database, a mouse embryo anatomy ontology has been created. A formalization of this anatomy is required to document its precise semantics and how it is used in the context of the Mouse Atlas. RESULTS: The paper describes the existing anatomy ontology and formalizes aspects of it using a predicate logic based approach. It therefore provides a guide for users of the current version of the ontology, as well as the basis for a description of the anatomy using an ontology language, such as OWL, thus enabling future work on reasoning about the Mouse Atlas in the context of an intelligent gene expression bioinformatics workflow system. The logic has been implemented in a Prolog prototype. AVAILABILITY: The Mouse Atlas is available on-line at http://genex.hgu.mrc.ac.uk

Algorithms↗

PubMed2006

Lectindb: a plant lectin database.

Lectins, a class of carbohydrate-binding proteins, are now widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes. They encompass different members that are diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities, and specificities as well as their larger biological roles and potential applications. It is not surprising, therefore, that the vast amount of experimental data on lectins available in the literature is so diverse, that it becomes difficult and time consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. To achieve an effective use of all the data toward understanding the function and their possible applications, an organization of these seemingly independent data into a common framework is essential. An integrated knowledge base ( Lectindb, http://nscdb.bic.physics.iisc.ernet.in ) together with appropriate analytical tools has therefore been developed initially for plant lectins by collating and integrating diverse data. The database has been implemented using MySQL on a Linux platform and web-enabled using PERL-CGI and Java tools. Data for each lectin pertain to taxonomic, biochemical, domain architecture, molecular sequence, and structural details as well as carbohydrate and hence blood group specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value not only for basic studies in lectin biology but also for basic studies in pursuing several applications in biotechnology, immunology, and clinical practice, using these molecules.

Algorithms↗

PubMed2026

Bioinformatics Analysis and Experimental Validation of Key Genes Associated With Hypoxia and Ischemia in Myocardial Infarction.

BACKGROUND: This study aimed to screen and identify core hypoxia-ischemia-related genes associated with myocardial infarction (MI). METHOD: Two transcriptomic datasets, GSE97320 and GSE48060, were retrieved from the Gene Expression Omnibus (GEO) database. After data integration and batch effect elimination, differential expression analysis was performed to screen differentially expressed genes (DEGs), and the corresponding visualization analysis was conducted. Hypoxia-ischemia-related genes were acquired from the GeneCards database; hypoxia-ischemia related genes (HIRGs) were subsequently identified by intersecting the retrieved genes with screened DEGs. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were implemented to explore the biological functions and underlying signaling pathways of HIRGs. A combination of protein-protein interaction (PPI) network analysis and random forest (RF) algorithm was applied to screen hub genes from HIRGs. The external GEO dataset GSE66360 was utilized to validate the expression patterns of candidate hub genes. Furthermore, an acute myocardial infarction (AMI) mouse model was established, and quantitative real-time polymerase chain reaction (qPCR) was performed to detect the mRNA expression levels of hub genes in myocardial tissues for in vivo validation. RESULTS: A total of 633 DEGs and 308 hypoxia-ischemia-related genes were screened in the present study, among which 21 overlapping HIRGs were obtained. PLAUR and IL1B were finally identified as two hub genes from HIRGs based on PPI network and random forest algorithm. The qPCR results revealed that the expression levels of PLAUR and IL1B were significantly upregulated in the AMI group compared with the sham operation group (p < 0.05). CONCLUSION: The present findings demonstrated that PLAUR and IL1B serve as pivotal genes involved in the pathological hypoxia-ischemia process of AMI. These two genes may act as novel biomarkers and promising therapeutic targets for the recognition and clinical intervention of hypoxia-ischemia injury following AMI.

Myocardial Infarction↗

PubMed2006

Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene.

Pyruvate, orthophosphate dikinase (PPDK; E.C. 2.7.9.1) catalyzes the synthesis of the primary inorganic carbon acceptor, phosphoenolpyruvate in the C4 photosynthetic pathway and is reversibly regulated by light. PPDK regulatory protein (RP), a bifunctional serine/threonine kinase-phosphatase, catalyzes both the ADP-dependent inactivation and the Pi-dependent activation of PPDK. Attempts to clone the RP have to date proven unsuccessful. A bioinformatics approach was taken to identify the nucleotide and amino acid sequence of the protein. Based on previously established characteristics including molecular mass, known inter- and intracellular location, functionality, and low level of expression, available databases were interrogated to ultimately identify a single candidate gene. In this paper, we describe the nucleotide and deduced amino acid sequence of this gene and establish its identity as maize PPDK RP by in vitro analysis of its catalytic properties via the cloning and expression of the recombinant protein.

Amino Acid Sequence↗

PubMed2005

Analyses of murine postsynaptic density-95 identify novel isoforms and potential translational control elements.

Postsynaptic density-95 (PSD-95) is an evolutionarily conserved synaptic adaptor protein that is known to bind many proteins including the NMDA receptor. This observation has implicated it in many NMDA receptor-dependent processes including spatial learning and synaptic plasticity. We have cloned and characterised the murine PSD-95 gene. In addition, we have identified two previously uncharacterised splice variants of the major murine PSD-95 transcript (PSD-95alpha): PSD-95alpha-2b results from an extension of exon 2 and PSD-95alpha-Delta18 from the temporal exclusion of exon 18. The presence of PSD-95alpha-2b sequences in other PSD-95 family members implicates this peptide stretch as functionally significant. Another potential transcript (PSD-95gamma) was also identified based on examination of EST databases. Immunoprecipitation assays demonstrate that proteins corresponding in size to PSD-95alpha-Delta18 and PSD-95gamma interact with the NMDA receptor, suggesting an important biological role for these isoforms. Finally, we have performed bioinformatics analyses of the PSD-95 mRNA untranslated regions, identifying multiple translational control elements that suggest protein production could be regulated post-transcriptionally. The variety of mRNA isoforms and regulatory elements identified provides for a high degree of diversity in the structure and function of PSD-95 proteins.

Age Factors↗

PubMed2004

PlantGDB, plant genome database and analysis tools.

PlantGDB (http://www.plantgdb.org/) is a database of molecular sequence data for all plant species with significant sequencing efforts. The database organizes EST sequences into contigs that represent tentative unique genes. Contigs are annotated and, whenever possible, linked to their respective genomic DNA. Genome sequence fragments are assembled similarly. The goal of the PlantGDB web site is to establish the basis for identifying sets of genes common to all plants or specific to particular species by integrating a number of bioinformatics tools that facilitate gene prediction and cross- species comparisons. For species with large-scale genome sequencing efforts, PlantGDB provides genome browsing capabilities that integrate all available EST and cDNA evidence for current gene models (for Arabidopsis thaliana, see the AtGDB site at http://www.plantgdb.org/AtGDB/).

Computational Biology↗

PubMed2006

PROMPT: a protein mapping and comparison tool.

BACKGROUND: Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly enriched in certain annotation attributes or sequence properties compared to another group, and whether this enrichment is statistically significant. In order to conduct such comparisons it is often required to integrate molecular sequence data and experimental information from disparate incompatible sources. While many specialized programs exist for comparisons of this kind in individual problem domains, such as expression data analysis, no generic software solution capable of addressing a wide spectrum of routine tasks in comparative proteomics is currently available. RESULTS: PROMPT is a comprehensive bioinformatics software environment which enables the user to compare arbitrary protein sequence sets, revealing statistically significant differences in their annotation features. It allows automatic retrieval and integration of data from a multitude of molecular biological databases as well as from a custom XML format. Similarity-based mapping of sequence IDs makes it possible to link experimental information obtained from different sources despite discrepancies in gene identifiers and minor sequence variation. PROMPT provides a full set of statistical procedures to address the following four use cases: i) comparison of the frequencies of categorical annotations between two sets, ii) enrichment of nominal features in one set with respect to another one, iii) comparison of numeric distributions, and iv) correlation of numeric variables. Analysis results can be visualized in the form of plots and spreadsheets and exported in various formats, including Microsoft Excel. CONCLUSION: PROMPT is a versatile, platform-independent, easily expandable, stand-alone application designed to be a practical workhorse in analysing and mining protein sequences and associated annotation. The availability of the Java Application Programming Interface and scripting capabilities on one hand, and the intuitive Graphical User Interface with context-sensitive help system on the other, make it equally accessible to professional bioinformaticians and biologically-oriented users. PROMPT is freely available for academic users from http://webclu.bio.wzw.tum.de/prompt/.

Computational Biology↗

PubMed2025

Analysis of ferroptosis-related genes in cerebral ischemic stroke via immune infiltration and single-cell RNA-sequencing.

Ischemic stroke (IS) represents a harmful neurological disorder with limited treatment options. Ferroptosis accounts for the iron-dependent, nonapoptotic cell death pattern, which shows the feature of fatal lipid ROS accumulation. Nonetheless, ferroptosis-related biomarkers for identifying IS early are currently lacking. The present study focused on investigating the possible ferroptosis-related biomarkers for IS and analyzing their effects on immune infiltration. Altogether five hub differentially expressed ferroptosis-related genes (DEFRGs) were identified from the relevant databases. Additionally, single-cell RNA-sequencing (seq) analysis was conducted for the comprehensive mapping of cell populations based on the IS database. These five hub DEFRGs were analyzed using gene set enrichment analysis, miRNA prediction, and single-cell RNA-seq analysis. A transient middle cerebral artery occlusion mouse model was constructed. We also adopted bioinformatics methods combined with western blot, changes to mitochondria, hematoxylin & eosin staining, Nissl staining, ROS fluorescence staining, immunohistochemistry, and quantitative real-time polymerase chain reaction (qRT-PCR) to show the involvement of ferroptosis in IS progression. The results revealed that nuclear factor erythroid-derived 2-like 2 (Nfe2l2) was the potential candidate biomarker for IS diagnosis, and ferroptosis may be suppressed via the Nfe2l2/HO-1 pathway. Thus, drug targeting Nfe2l2 can shed novel lights on IS treatment.

Ferroptosis↗

PubMed1998

The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining.

MOTIVATION: To make effective use of the vast amounts of expressed sequence tag (EST) sequence data generated by the Merck-sponsored EST project and other similar efforts, sequences must be organized into gene classes, and scientists must be able to 'mine' the gene class data in the context of related genomic data. RESULTS: This paper presents the Merck Gene Index browser, an easily extensible, World Wide Web-based system for mining the Merck Gene Index (MGI) and related genomic data. The MGI is a non-redundant set of clones and sequences, each representing a distinct gene, constructed from all high-quality 3' EST sequences generated by the Merck-sponsored EST project. The MGI browser integrates data from a variety of sources and storage formats, both local and remote, using an eclectic integration strategy, including a federation of relational databases, a local data warehouse and simple hypertext links. Data currently integrated include: LENS cDNA clone and EST data, dbEST protein and non-EST nucleic acid similarity data, WashU sequence chromatograms. Entrez sequence and Medline entries, and UniGene gene clusters. Flatfile sequence data are accessed using the Bioapps server, an internally developed client-server system that supports generic sequence analysis applications. Browser data are retrieved and formatted by means of the Bioinformatics Data Integration Toolkit (B-DIT), a new suite of Perl routines.

Abstracting and Indexing↗

PubMed2026

Next-Generation Sequencing-Based High-Resolution Typing of HLA-A, -B, -C and HPA Genes in Jilin Province: Building a Platelet Donor Database and Identifying Novel Alleles.

To systematically analyse HLA-A, -B and -C and human platelet antigen (HPA) genotypes of platelet donors in Jilin Province using next-generation sequencing (NGS) technology, a comprehensive donor database was established. Additionally, potential novel alleles were identified, providing a scientific basis for enhancing the safety of clinical blood transfusions. DNA fragments from 200 platelet donor samples in Jilin Province were amplified using locus-specific primers. Comprehensive sequencing of HLA and HPA genes was performed via NGS. Bioinformatics analysis was employed to process genotyping results and screen for novel genetic variants. Newly discovered alleles were validated by Sanger sequencing to ensure accuracy and reliability. HLA genotyping achieved three-field allele resolution, revealing the highest-frequency alleles are as follows: HLA-A*11:01:01, HLA-B*13:02:01, HLA-C*01:02:01 and C*03:04:01. A novel allele B*49:91 (mutation: E2 24T>C) was identified. For the HPA systems (HPA-1, -2, -3, -5, -6, -15, -21), high heterozygosity was observed in HPA-3 and HPA-15, while no bb homozygosity was detected in HPA-1, -2, -5, -6 or -21. The application of NGS in constructing a platelet HLA/HPA gene database enables high-resolution genotyping, laying a critical foundation for precise platelet matching. This significantly reduces the risk of platelet transfusion refractoriness (PTR) and facilitates the discovery of novel allelic variants. The database provides essential theoretical and practical guidance for future donor screening and personalised transfusion strategies.

Humans↗

PubMed2004

Normal/disease-paired cDNA library subtraction for molecular marker development.

This study consists of a novel strategy for the identification of potential cancer exclusively expressed genes, which might lead to the development of valuable diagnostic molecular markers. Normal- and cancer-paired tissues from the same patient were collected and subjected to the construction of primary complementary deoxyribonucleic acid (cDNA) libraries. The cancer cDNA library was generated by subtracting normal cDNAs from the primary cancer library. The remaining clones in the subtracted cancer library were sequenced and Basic Local Alignment Search Tool (BLAST)-analyzed against current nonredundant and est_human databases in the GenBank. The clones that had no matches with any known gene sequences except the human genomic sequences were identified as ideal candidates for potential molecular marker development. The candidate marker sequence and associated primer sequences were identified on the target clone sequence of the region with the least, or no, matched homologs. The specificity of the markers was measured by a polymerase chain reaction test experiment with the DNA templates from different human normal tissues, genomic DNA, and additional patients' tissues. Results from bioinformatical and experimental approaches used suggest that the methodology has a high potential to identify cancer exclusive transcripts. Thus, it might result in the development of diagnostic markers.

Biotechnology↗

PubMed2006

ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.

ParameciumDB (http://paramecium.cgm.cnrs-gif.fr) is a new model organism database associated with the genome sequencing project of the unicellular eukaryote Paramecium tetraurelia. Built with the core components of the Generic Model Organism Database (GMOD) project, ParameciumDB currently contains the genome sequence and annotations, linked to available genetic data including the Gif Paramecium stock collection. It is thus possible to navigate between sequences and stocks via the genes and alleles. Phenotypes, of mutant strains and of knockdowns obtained by RNA interference, are captured using controlled vocabularies according to the Entity-Attribute-Value model. ParameciumDB currently supports browsing of phenotypes, alleles and stocks as well as querying of sequence features (genes, UniProt matches, InterPro domains, Gene Ontology terms) and of genetic data (phenotypes, stocks, RNA interference experiments). Forms allow submission of RNA interference data and some bioinformatics services are available. Future ParameciumDB development plans include coordination of human curation of the near 40 000 gene models by members of the research community.

Alleles↗

PubMedDate not supplied

Automated protein identification by tandem mass spectrometry: issues and strategies.

Protein identification by tandem mass spectrometry (MS/MS) is key to most proteomics projects and has been widely explored in bioinformatics research. Obtaining good and trustful identification results has important implications for biological and clinical work. Although well matured, automated software identification of proteins from MS/MS data still faces a number of obstacles due to the complexity of the proteome or procedural issues of mass spectrometry data acquisition. Expected or unexpected modifications of the peptide sequences, polymorphisms, errors in databases, missed or non-specific cleavages, unusual fragmentation patterns, and single MS/MS spectra of multiple peptides of the same m/z are so many pitfalls for identification algorithms. A lot of research work has been carried out in recent years that yielded new strategies to handle a number of these issues. Multiple MS/MS identification algorithms are now available or have been theoretically described. The difficulty resides in choosing the most adapted method for each type of spectra being identified. This review presents an overview of the state-of-the-art bioinformatics approaches to the identification of proteins by MS/MS to help the reader doing the spade work of finding the right tools among the many possibilities offered.

Automation↗

PubMed2026

Bioinformatic analysis reveals the potential association of ESRP1 with the splicing of cytoskeleton-associated genes in doxorubicin-resistant MCF7 breast cancer cells.

BACKGROUND: Breast cancer remains one of the most prevalent malignancies among women, with doxorubicin resistance posing a significant challenge that undermines treatment success and survival outcomes. Aberrant alternative splicing (AS), driven by dysregulation or mutations in splicing factors (SFs), is implicated in cancer initiation, progression, and drug resistance. This study aims to investigate the association of the epithelial cell-specific splicing factor ESRP1 with doxorubicin resistance in breast cancer, focusing on how ESRP1 deficiency correlates with AS changes that promote chemoresistance. METHODS: We analyzed RNA-sequencing (RNA-seq) data from doxorubicin-resistant (MCF7-DR) and parental (MCF7) breast cancer cell lines to identify enhanced alternative splicing events (ASEs) and changes in ESRP1 expression; we further leveraged The Cancer Genome Atlas (TCGA)-BRCA cohort to construct an SF-RASE correlation network for screening core SFs (including ESRP1). An integrative analysis combining crosslinking immunoprecipitation (CLIP-seq) data and The Cancer Genome Atlas (TCGA) database was performed to validate ESRP1 binding targets and assess the association between ESRP1-related splicing and cytoskeleton organization. RESULTS: We observed extensive AS changes and significantly downregulated ESRP1 expression in MCF7-DR cells. Integrative analysis identified 61 high-confidence ASEs that correlate with ESRP1 expression. Further bioinformatic integration suggests that ESRP1 expression is associated with the splicing patterns of SPTBN1, MAP2K7, FGFR3, and CYB561A3-four genes involved in cytoskeleton organization-though direct experimental verification to confirm a causal regulatory relationship between ESRP1 and the splicing of these genes is still pending. CONCLUSIONS: Our findings suggest that ESRP1 expression is closely associated with doxorubicin resistance in breast cancer cells, with concomitant alterations in key ASEs linked to cytoskeletal remodeling that correlate with ESRP1. Exploring the ESRP1-related splicing network may offer new strategies to overcome chemoresistance and improve patient outcomes. However, the small cell line sample size (n = 2 per group) constrains the robustness of ASE and SF-ASE correlation findings, and these results should be interpreted with caution and require further validation with larger sample cohorts.

Alternative splicing↗

PubMed2001

Identification of the human crooked neck gene by comparative gene identification.

Drosophila melanogaster serves as a useful model organism for functional genomic studies, and its genome project was recently completed. We previously described a comparative-gene-identification approach to assist human ortholog gene identification that involves applying an entire proteome as an alignment template. Analysis of the available 14100 Drosophila protein sequences revealed that 37% of them (5228 sequences) might lead to discoveries of novel human genes. Upon further database interrogations, we found several putative full-length human gene transcripts, including the human crooked neck (crn) gene. Based on sequence gap-closure experiments using reverse transcriptase-polymerase chain reaction as well as bioinformatic analysis, we found that the assembled human cDNA contig of crooked neck gene was at least 3903 base pairs in length with alternative splicing variations which encoded mainly for a 687-amino-acid residue protein. The human crooked neck gene was located on chromosome 20 with at least 15 exons. The unique features of the 16 copies of the tetratrico peptide repeat (TPR) motif were conserved in the yeast, fly and human crooked neck orthologous proteins, which were important for spliceosome assembly in cells.

Amino Acid Sequence↗

PubMed2001

Ontologies of developmental anatomy: their current and future roles.

A central problem in current biology is elucidating the molecular networks that drive developmental change and physiological function. Such knowledge is needed partly to understand these networks, partly to be able to manipulate them, and partly to understand and help treat those human congenital abnormalities that arise as a result of mutation. Thus far, bioinformatics technology has been of limited use in this enterprise, mainly because its core focus has been on sequence technology and data archiving. For bioinformatics to be of use in this next tier of investigations, genetic and protein data need to be both archived and searchable by tissue since this is the level at which these networks operate. The resulting databases in turn require ontologies of developmental anatomy that can provide the formal infrastructure for handling gene expression, microarray and other tissue-based data. Here, the progress in making such ontologies, particularly for the developing mouse, is reported and the uses to which they are and will be put, together with the resources and tools currently available for investigating molecular networks and the genetic basis of congenital abnormalities, are considered.

Anatomy↗

PubMed2005

The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

BACKGROUND: The uptake of nutrients, expulsion of metabolic wastes and maintenance of ion homeostasis by the intraerythrocytic malaria parasite is mediated by membrane transport proteins. Proteins of this type are also implicated in the phenomenon of antimalarial drug resistance. However, the initial annotation of the genome of the human malaria parasite Plasmodium falciparum identified only a limited number of transporters, and no channels. In this study we have used a combination of bioinformatic approaches to identify and attribute putative functions to transporters and channels encoded by the malaria parasite, as well as comparing expression patterns for a subset of these. RESULTS: A computer program that searches a genome database on the basis of the hydropathy plots of the corresponding proteins was used to identify more than 100 transport proteins encoded by P. falciparum. These include all the transporters previously annotated as such, as well as a similar number of candidate transport proteins that had escaped detection. Detailed sequence analysis enabled the assignment of putative substrate specificities and/or transport mechanisms to all those putative transport proteins previously without. The newly-identified transport proteins include candidate transporters for a range of organic and inorganic nutrients (including sugars, amino acids, nucleosides and vitamins), and several putative ion channels. The stage-dependent expression of RNAs for 34 candidate transport proteins of particular interest are compared. CONCLUSION: The malaria parasite possesses substantially more membrane transport proteins than was originally thought, and the analyses presented here provide a range of novel insights into the physiology of this important human pathogen.

Amino Acid Sequence↗

PubMed2004

Fast and effective prediction of microRNA/target duplexes.

MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate the expression of target genes by binding to the target mRNAs. Although a large number of animal miRNAs has been defined, only a few targets are known. In contrast to plant miRNAs, which usually bind nearly perfectly to their targets, animal miRNAs bind less tightly, with a few nucleotides being unbound, thus producing more complex secondary structures of miRNA/target duplexes. Here, we present a program, RNA-hybrid, that predicts multiple potential binding sites of miRNAs in large target RNAs. In general, the program finds the energetically most favorable hybridization sites of a small RNA in a large RNA. Intramolecular hybridizations, that is, base pairings between target nucleotides or between miRNA nucleotides are not allowed. For large targets, the time complexity of the algorithm is linear in the target length, allowing many long targets to be searched in a short time. Statistical significance of predicted targets is assessed with an extreme value statistics of length normalized minimum free energies, a Poisson approximation of multiple binding sites, and the calculation of effective numbers of orthologous targets in comparative studies of multiple organisms. We applied our method to the prediction of Drosophila miRNA targets in 3'UTRs and coding sequence. RNAhybrid, with its accompanying programs RNAcalibrate and RNAeffective, is available for download and as a Web tool on the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/).

3' Untranslated Regions↗