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PubMed2024

Identification of autophagy-related genes as potential biomarkers correlated with immune infiltration in bipolar disorder: a bioinformatics analysis.

BACKGROUND: Bipolar disorder (BPD) is a kind of manic and depressive phase alternate episodes of serious mental illness, and it is correlated with well-documented cortical brain abnormalities. Emerging evidence supports that autophagy dysfunction in neuronal system contributes to pathophysiological changes in neurological disease. However, the role of autophagy in bipolar disorder has rarely been elucidated. This study aimed to identify the autophagy-related gene as a potential biomarker Correlated to immune infiltration in BPD. METHODS: The microarray dataset GSE23848 and autophagy-related genes (ARGs) were downloaded. Differentially expressed genes (DEGs) between normal and BPD samples were screened using the R software. Machine learning algorithms were performed to screen the significant candidate biomarker from autophagy-related differentially expressed genes (ARDEGs). The correlation between the screened ARDEGs and infiltrating immune cells was explored through correlation analysis. RESULTS: In this study, the autophagy pathway was abundantly enriched and activated in BPD, as indicated by Pathway enrichment analysis. We identified 16 ARDEGs in BPD compared to the normal group. A signature of 4 ARDEGs (ERN1, ATG3, CTSB, and EIF2AK3) was screened. ROC analysis showed that the above genes have good diagnostic performance. In addition, immune correlation analysis considered that the above four genes significantly correlated with immune cells in BPD. CONCLUSIONS: Autophagy - immune cell axis mediates pathophysiological changes in BPD. Four important ARDEGs are prospective to be potential biomarkers associated with immune infiltration in BPD and helpful for the prediction or diagnosis of BPD.

Bipolar Disorder↗
PubMed2025

Bioinformatics identification and validation of pyroptosis-related gene for ischemic stroke.

BACKGROUND: Ischemic stroke (IS) is one of the common and frequent diseases with extremely high lethality and disability in the world, and there is no effective treatment at present. This study aimed to screen hub genes involved in cerebral ischemia/reperfusion injury (CIRI) and pyroptosis, and explore promising intervention targets. METHODS: CIRI-related genes (GSE202659 and GSE131193) and pyroptosis-related genes (PRGs) in mice were obtained from the Gene Expression Omnibus (GEO) and GeneCards database. We screened for LASSO regression to construct a prognostic model of GSE131193 and PRGs and examined by GSE137482. The functional enrichment analysis of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were performed on pyroptosis-related differentially expressed genes (PRDEGs) of GSE202659.The key modules for CIRI and pyroptosis were identified by Weight Gene Co-expression Network Analysis (WGCNA). Subsequently, Protein-protein Interaction (PPI) network and the Cytoscape was constructed to screen out hub genes. Used the starBase to predict miRNA interacting with hub genes and constructed mRNA-miRNA-lncRNA interaction networks. CIRI-related Molecular Subtypes were constructed for hub genes. The relationship between immune cells and hub genes was verified via CIBERSORT. Finally, we selected C57BL/6 mice to construct models to confirm hub genes by enzyme linked immunosorbent assay (ELISA), reverse transcription-polymerase chain reaction (RT-PCR), western blot, and Immunofluorescence. RESULTS: A total of 272 PRGs and 35 PRDEGs were screened. An eight-gene risk prediction models were established (AUC = 0.868). GO, KEGG, GSEA and GSVA analyses revealed that PRDEGs were mainly involved in positive regulation of cytokine production, and NOD-like receptor signaling pathway. And then, seven hub genes (Irf1, Icam1, Tlr2, Tnf, Cebpb, Il1rn, and Casp8) were identified by PPI. Icam1, Tnf, Cebpb, Il1rn, and Casp8 had high expression profiles in Cluster2 by hierarchical clustering. The immune infiltration analysis results showed that among the hub genes, Cebpb, Il1rn, and Casp8, showed a significant positive correlation with the degree of NK.Actived, and Icam1 showed a significant negative correlation with B.Cells.Memory. The results of animal experiments significantly demonstrated an upregulation of Irf1, Icam1, Tlr2, Cebpb, and Il1rn. CONCLUSION: Our finding indicated that Irf1, Icam1, Tlr2, Cebpb, and Il1rn are hub genes associated with pyroptosis, and these genes are all associated with different immune cells, so as to provide new targets for the prevention and treatment of IS from the perspective of pyroptosis.

Pyroptosis↗
PubMed2026

An open-source clinical bioinformatics pipeline for real-world NGS implementation: translating genomic variants into actionable treatment strategies in oncology.

BACKGROUND: Next-Generation Sequencing (NGS) has become a cornerstone technology in clinical practice, yet its adoption presents significant challenges. Physicians and oncologists must manage vast amounts of genome-scale data and transform it into actionable insights for complex decision-making. While commercial systems exist to synthesize data from NGS experiments into clinical reports, many are hindered by limitations such as closed-source designs that restrict transparency and customization. Additionally, some fail to leverage publicly available genomic databases, missing opportunities to integrate valuable external data. Furthermore, the rigidity of many tools in accommodating diverse NGS panels limits their applicability across varied clinical scenarios. METHODS: To address these limitations, we developed OncoReport, an open-source tool that generates comprehensive reports from NGS analyses. By integrating publicly accessible databases, OncoReport provides a robust, user-friendly environment equipped with essential tools for NGS analysis. This design aims to enhance data interpretation and support informed clinical decision-making. RESULTS: Rigorous testing has demonstrated OncoReport’s effectiveness in producing detailed, actionable reports that are clear and easy to use. By automating key aspects of the workflow, the tool significantly reduces manual effort and expedites the synthesis and interpretation of NGS results, making genomic insights more accessible to clinicians. CONCLUSION: OncoReport offers a transparent, flexible, and efficient framework for clinicians to analyze and apply genomic data in patient care. By streamlining workflows and leveraging open-source principles, it empowers healthcare professionals to make informed, data-driven decisions. OncoReport is freely available at https://oncoreport.atlas.dmi.unict.it, with source code and issue tracking on GitHub: https://github.com/knowmics-lab/oncoreport .

Humans↗
PubMed2005

Bioinformatic analysis of peptide precursor proteins.

Neuropeptides are among the most important signal molecules in animals. Traditional identification of peptide hormones through peptide purification is a tedious and time-consuming process. With the advent of the genome sequencing projects, putative peptide precursor can be mined from the genome. However, because bioactive peptides are usually quite short in length and because the active core of a peptide is often limited to only a few amino acids, using the BLAST search engine to identify neuropeptide precursors in the genome is difficult and sometimes impossible. To overcome these shortcomings, we subject the entire set of all known Drosophila melanogaster peptide precursor sequences to motif-finding algorithms in search of a motif that is common for all prepropeptides and that could be used in the search for new peptide precursors.

Amino Acid Sequence↗
PubMed2004

Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics.

In 2002-2003, the American College of Medical Informatics (ACMI) undertook a study of the future of informatics training. This project capitalized on the rapidly expanding interest in the role of computation in basic biological research, well characterized in the National Institutes of Health (NIH) Biomedical Information Science and Technology Initiative (BISTI) report. The defining activity of the project was the three-day 2002 Annual Symposium of the College. A committee, comprised of the authors of this report, subsequently carried out activities, including interviews with a broader informatics and biological sciences constituency, collation and categorization of observations, and generation of recommendations. The committee viewed biomedical informatics as an interdisciplinary field, combining basic informational and computational sciences with application domains, including health care, biological research, and education. Consequently, effective training in informatics, viewed from a national perspective, should encompass four key elements: (1). curricula that integrate experiences in the computational sciences and application domains rather than just concatenating them; (2). diversity among trainees, with individualized, interdisciplinary cross-training allowing each trainee to develop key competencies that he or she does not initially possess; (3). direct immersion in research and development activities; and (4). exposure across the wide range of basic informational and computational sciences. Informatics training programs that implement these features, irrespective of their funding sources, will meet and exceed the challenges raised by the BISTI report, and optimally prepare their trainees for careers in a field that continues to evolve.

Computational Biology↗
PubMed2000

Human proton/oligopeptide transporter (POT) genes: identification of putative human genes using bioinformatics.

The proton-dependent oligopeptide transporters (POT) gene family currently consists of approximately 70 cloned cDNAs derived from diverse organisms. In mammals, two genes encoding peptide transporters, PepT1 and PepT2 have been cloned in several species including humans, in addition to a rat histidine/peptide transporter (rPHT1). Because the Candida elegans genome contains five putative POT genes, we searched the available protein and nucleic acid databases for additional mammalian/human POT genes, using iterative BLAST runs and the human expressed sequence tags (EST) database. The apparent human orthologue of rPHT1 (expression largely confined to rat brain and retina) was represented by numerous ESTs originating from many tissues. Assembly of these ESTs resulted in a contiguous sequence covering approximately 95% of the suspected coding region. The contig sequences and analyses revealed the presence of several possible splice variants of hPHT1. A second closely related human EST-contig displayed high identity to a recently cloned mouse cDNA encoding cyclic adenosine monophosphate (cAMP)-inducible 1 protein (gi:4580995). This contig served to identify a PAC clone containing deduced exons and introns of the likely human orthologue (termed hPHT2). Northern analyses with EST clones indicated that hPHT1 is primarily expressed in skeletal muscle and spleen, whereas hPHT2 is found in spleen, placenta, lung, leukocytes, and heart. These results suggest considerable complexity of the human POT gene family, with relevance to the absorption and distribution of cephalosporins and other peptoid drugs.

Blotting, Northern↗
PubMed2002

Bioinformatic analysis of the human mu opioid receptor (OPRM1) splice and polymorphic variants.

Mu opioid receptor (OPRM1), a member of the G-protein coupled receptor superfamily, mediates the analgesic and euphoric effects of opioid drugs. The sequences of OPRM1 cDNA and reported splice variants were used to search the public and Celera genomic databases. The matched sequences were analyzed to assemble an OPRM1 genomic contig. Human OPRM1 gene was estimated to span at least 90 kb in the chromosome 6q24-25 region. Four coding exons are separated by 3 introns. While intron 2 has only 773 bp, these databases for the first time provide the precise length of and other information about long introns 1 and 3, containing 50 and 27 kb, respectively. When a consensus exon/intron splice junction at the end of the coding exon 3 was not utilized, it may have resulted in continuous translation of the exon to yield the splice variant OPRM1A. The study did not identify human orthologs of other OPRM1 variants that had been reported for mouse OPRM1, although several proposed exons were found to be included in mouse genomic clones. Single nucleotide polymorphisms in the OPRM1 gene were also analyzed and summarized, which could provide potential polymorphic markers for molecular genetic studies.

Alternative Splicing↗
PubMed2005

[Bioinformatics].

Explore the source record for details and available documents.

Amino Acid Sequence↗
PubMed2005

Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation.

Polyadenylation is an essential step for the maturation of almost all cellular mRNAs in eukaryotes. In human cells, most poly(A) sites are flanked by the upstream AAUAAA hexamer or a close variant, and downstream U/GU-rich elements. In yeast and plants, additional cis elements have been found to be located upstream of the poly(A) site, including UGUA, UAUA, and U-rich elements. In this study, we have developed a computer program named PROBE (Polyadenylation-Related Oligonucleotide Bidimensional Enrichment) to identify cis elements that may play regulatory roles in mRNA polyadenylation. By comparing human genomic sequences surrounding frequently used poly(A) sites with those surrounding less frequently used ones, we found that cis elements occurring in yeast and plants also exist in human poly(A) regions, including the upstream U-rich elements, and UAUA and UGUA elements. In addition, several novel elements were found to be associated with human poly(A) sites, including several G-rich elements. Thus, we suggest that many cis elements are evolutionarily conserved among eukaryotes, and human poly(A) sites have an additional set of cis elements that may be involved in the regulation of mRNA polyadenylation.

Computational Biology↗
PubMed2026

Toward a unified approach: Considerations for bioinformatic and sequencing activities & data in wastewater surveillance of biologic public health threats.

Genomic technologies such as PCR and next-generation sequencing (NGS) have greatly advanced public health surveillance, especially during COVID-19, by enabling detailed tracking of pathogen spread, origins, and variants. While PCR is vital for targeted detection, falling NGS costs have made large-scale, high-throughput sequencing more feasible, supporting broader pathogen monitoring-including the detection of vaccine escape variants and new strains. Applying NGS to wastewater offers valuable population-level insights but faces challenges such as variable sample complexity, the need for skilled staff, suitable platforms, and robust IT infrastructure. Although there are currently a lot of efforts towards defining guidelines for sampling, analysis, and integrating wastewater data into public health policy, such as the recently published International Cookbook for Wastewater Practitioners, they often lack universal applicability, emphasizing the analytical approaches in favour of the NGS-based approaches. However, standardising protocols for sampling, sequencing, and analysis is crucial to ensure reliable, comparable data across surveillance systems worldwide. Pilot studies and continuous refinement are recommended to overcome implementation hurdles and fully realise the benefits of NGS in wastewater surveillance. This work attempts to outline these challenges and opportunities across the entire wastewater surveillance workflow, from data generation to reporting, and provide some concrete suggestions and considerations across the spectrum of activities. We further highlight that the infrastructure, funding and government-policy context in which surveillance operates acts as an enabling condition for these activities, and that technical standardisation alone is unlikely to deliver durable, comparable surveillance in its absence.

considerations↗
PubMed2004

A novel zinc-containing alpha-keto ester reductase from actinomycete: an approach based on protein chemistry and bioinformatics.

We have achieved the purification of an alpha-keto ester reductase (SCKER) from S. coelicolor A3(2) whole cells. SCKER proved to be a homotetramer of 132 kDa containing one equivalent of zinc ion per subunit. The enzyme differed from other alpha-keto ester reductases from microorganisms with regard to subunit structure and metal ion dependency. From a computer search using the protein data banks, the N-terminal amino acid sequence of SCKER was consistent with that of a possible zinc containing alcohol dehydrogenase in S. coelicolor A3(2). None of three hypothetical proteins of S. coelocor A3(2) having a high homology sequence with those of already purified alpha-keto ester reductases from S. thermocyaneoviolaceus [Yamaguchi, H., et al., Biosci. Biotechnol. Biochem., 66, 588-597 (2002)] was identical with that of SCKER.

Alcohol Dehydrogenase↗
PubMed2003

Bioinformatic insight into the unity and diversity of cytochromes P450.

For the past few decades, cytochromes P450 (CYPs) have been the subject of extensive research, owing to the ability of these enzymes to serve as drug targets as well as to their active participation in drug metabolism. Other varieties and functions of CYPs have been discovered and this superfamily currently comprises over 2000 different protein species. In the present study, the protein sequences of CYPs were submitted to computer analysis for elucidation of the structural basis of their pronounced functional diversity. The basic local alignment search tool (BLAST) was used to demonstrate that CYP protein sequences share a certain general similarity; at the same time, it was shown that the CYP superfamily may be split into a number of groups of intimately related proteins. These groups, the families, were revealed by means of cluster analysis, which demonstrated a strong hierarchy among the animal, bacterial and fungal P450s, and the lack of such a hierarchy for plant enzymes. Multiple alignment and consensus sequence analysis were the approaches taken to find out which structural peculiarities of P450s are responsible for the deviations from the random picture. Proteins within each family were aligned and collapsed to the corresponding consensus sequences, the alignment of which produced the consensus for the whole superfamily. The latter consensus yielded a number of unity motifs (most of which being related to the heme-fixing assembly), while the cross-family comparison of consensus sequences enabled the retrieval of some diversity motifs. Three consensus sequences (for the CYP51 and CYP2 families and for the superfamily) were compared, to line up the unity and diversity motifs with the appropriate X-ray data.

Amino Acid Sequence↗