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PubMedDate not supplied

The construction and assessment of a statistical model for the prediction of protein assay data.

The focus of this work is the development of a statistical model for a bioinformatics database whose distinctive structure makes model assessment an interesting and challenging problem. The key components of the statistical methodology, including a fast approximation to the singular value decomposition and the use of adaptive spline modeling and tree-based methods, are described, and preliminary results are presented. These results are shown to compare favorably to selected results achieved using comparitive methods. An attempt to determine the predictive ability of the model through the use of cross-validation experiments is discussed. In conclusion a synopsis of the results of these experiments and their implications for the analysis of bioinformatic databases in general is presented.

Computational Biology↗

PubMed2026

Exploring Endoplasmic Reticulum Stress-Related Genes in Cartilage Defects: Implications for Diagnosis and Therapy.

INTRODUCTION: Cartilage defects (CDs) are orthopedic conditions with limited regenerative potential. This study aimed to identify endoplasmic reticulum (ER) stress-related biomarkers and construct a diagnostic model to enhance the early detection of CD. METHODS: This study analyzed the transcriptomic dataset GSE129147 to identify ER stressrelated differentially expressed genes (ERSRDEGs) between CD and control tissues using the limma package (version 3.58.1). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were employed for functional enrichment. Immune infiltration was assessed using cell-type identification, which involved estimating the relative subsets of RNA transcripts and single-sample gene set enrichment analysis. Diagnostic models were constructed using logistic regression, support vector machine, and least absolute shrinkage and selection operator regression. RESULTS: Twenty ERSRDEGs were identified, with CYBB, ATP6V1A, and TNFRSF12A significantly upregulated in CD samples. GO and KEGG analyses highlighted oxidative stress response and extracellular matrix remodeling as key mechanisms in CD pathogenesis. Immune analysis revealed an increase in regulatory T cells and a reduction in CD8. T cells. TNFRSF12A showed strong immune associations and, together with TWIST1 and ATP6V1A, formed the final preliminary diagnostic model. The preliminary LASSO model achieved satisfactory predictive accuracy (AUC: 0.7-0.9). DISCUSSION: These findings suggest that ER stress and immune imbalance jointly contribute to cartilage degeneration. The identified genes, particularly TNFRSF12A, TWIST1, and ATP6V1A, not only serve as potential biomarkers but also provide preliminary evidence for new mechanistic insights into stress-immune crosstalk in CD. CONCLUSION: This study reveals the key roles of ER stress and immune dysregulation in CDs. Moreover, the ERSRDEG-based diagnostic model provides preliminary bioinformatics evidence and potential molecular indicators for targeted diagnostics and therapies.

Humans↗

PubMed2026

New insights into diagnostic values and mechanisms of ferroptosis associated with immune infiltration in diabetic kidney disease.

The pathogenesis of diabetic kidney disease (DKD) is complex and closely related to ferroptosis and immune dysregulation, but the relevance is unclear. The present study investigates the potential mechanisms of ferroptosis-related genes (FRGs) in DKD and their relationship with the immune-inflammatory response. It searches for new diagnostic biomarkers to help diagnose and treat DKD. Four Gene Expression Omnibus (GEO) datasets, GSE30528, GSE30529 and GSE30122 as the test set, and GSE96804 for validation, were analyzed. FRGs were obtained from GeneCards, and 47 ferroptosis-related differentially expressed genes (FRDEGs) were identified by intersecting with DKD-related differentially expressed genes. Functional enrichment analyses, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Gene Set Enrichment Analysis and Gene Set Variation Analysis, revealed that these FRDEGs are primarily associated with ferroptosis, hypoxia response and immune inflammation. Subsequently, the weighted gene co-expression network analysis (WGCNA) was employed to expand the ferroptosis-related gene network, and intersection of the 47 FRDEGs with key WGCNA module genes yielded 10 key genes. Based on the 10 key genes, the least absolute shrinkage and selection operator and support vector machine algorithms identified three hub genes [chemokine ligand 5 (CCL5), forkhead box C1 (FOXC1) and lactotransferrin (LTF)] for DKD diagnosis. Receiver operating characteristic curves confirmed their diagnostic value, with FOXC1 and LTF validated in the independent dataset. Immune infiltration analysis via CIBERSORT revealed eight immune cell types with significantly different infiltration levels between the DKD and control group in the integrated GEO datasets. Notably, both LTF and CCL5 showed a significant positive correlation with gamma delta T cells (γδT). Quantitative PCR results confirmed differential expression of the three hub genes in the DKD group, with elevated expression observed in DKD mice following intervention with rosiglitazone and hyperoside.

bioinformatics analysis↗

PubMed2026

IL1B-centered immune dysregulation involving IL7R, CCR7, ITGB2 and IRF1 across insomnia and inflammatory bowel disease.

BACKGROUND: Insomnia is a prevalent sleep disorder that strongly affects one's quality of life and physical well-being. Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the intestines, and a majority of IBD patients suffer from comorbid insomnia. However, the shared molecular features linking insomnia and IBD remain poorly characterized. METHODS: Common differentially expressed genes (DEGs) were identified in datasets of insomnia (GSE208668) and IBD (GSE179285) using the Limma package. Functional enrichment was performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Protein-protein interaction (PPI) network construction and hub gene identification was subsequently performed. Furthermore, we validated the reliability of the hub genes using qRT-PCR and Enzyme-linked immunosorbent assay (ELISA). In addition, we constructed a TF-miRNA regulatory network of hub genes and assessed the abundance of immune cell infiltration in insomnia and IBD using CIBERSORT, EPIC, and xCell algorithms. Finally, we utilized the DsigDB to predict potential therapeutic candidates. RESULTS: The analysis revealed 75 upregulated and 32 downregulated common DEGs. Functional enrichment analysis revealed the inflammatory response and immune activation as pivotal drivers underlying the pathogenesis of both insomnia and IBD. Five hub DEGs, namely, IL1B, IL7R, CCR7, ITGB2, and IRF1, were subsequently screened and validated. The TF-miRNA-mRNA regulatory network consisted of 5 TFs, 14 miRNA nodes and 5 core mRNA nodes. Immune cell infiltration analysis revealed several patterns shared between insomnia and IBD. Additionally, 10 potential therapeutic drugs for insomnia and IBD were proposed. CONCLUSION: Integrative coexpression network analysis reveals convergent dysregulation of an IL1B-centered immune module (comprising IL7R, CCR7, ITGB2, and IRF1) across insomnia and IBD, a shared immune disturbance and candidate targets for simultaneous intervention upon further mechanistic validation.

Humans↗

PubMed2003

Cloning and sequence analysis of tumor-associated gene hMMTAG2 from human multiple myeloma cell line ARH-77.

In order to look for the tumor-associated genes from human multiple myeloma (MM), a cDNA library of human multiple myeloma cell line ARH-77 was constructed with eukaryote expression vector pcDNA3.1(+). The length of inserted fragments in library was 1.2 kb in average. All clones in cDNA library were transferred in situ to nylon membrane, which was divided into eight equal parts (A-H) and cultured in LB medium to set up gene pools. The plasmids in cDNA library and in gene pools were extracted and NIH/3T3 cells were transfected respectively. By G418 screening and colonies counting, gene pool A was chosen for the second cycle transfection. After several cycles, a clone, A62-17, was obtained, which had significant transforming ability. The length of this clone was 993 bp. The RACE technique was used for rapid amplification of A62-17 5'-end. The full length of this sequence has 1300 bp and was named as hMMTAG2 gene. hMMTAG2 consists of 8 exons and codes for a polypeptide of 263 amino acids (the accession number in GenBank: AY137773). It was located at chromosome 1q42.13. hMMTAG2 had same transforming activities in NIH/3T3 cells as the clone A62-17, and the number of transformant foci was 6 folds more than the blank vector pcDNA3.1(+). The analysis of bioinformatics revealed that hMMTAG2 had many phosphorylation sites for several protein kinases, N-myristoylation sites and nuclear localization signals, so it may be a signal molecule in the nucleus.

3T3 Cells↗

PubMed2006

[Analyzing the function of different expression genes in the brain of rat exposure to methylmercury using genomics technology].

OBJECTIVE: Analyzing the function of different expression genes in the brain of rat exposure to methylmercury. METHODS: The experimental group of rats were treated with 0.5 mg/kg weight of methylmercury via hypodermic injection. The different expression genes were scanned by using cDNA microarray, and the function genes were analyzed using genomics technology. RESULTS: The gene expression profiles showed that there were 303 genes, in which 170 were upregulated and 133 were downregulated, were differential expressed in the experimental group. Further analysis by bioinformatic technique disclosed that the differentially expressed genes were involved in many biological processes, which included immuno-response and detoxifcation, transfer and expression of genetic information, cell signalling, neurotransduction, cell proliferation and cell differentiation, apoptosis, etc. Cell signaling gene and neurotransduction gene had an very obvious change in the exposure group. CONCLUSION: The signaling pathway was the target by which methylmercury exerted the neurotoxic effects.

Animals↗

PubMed2026

Transcriptomic analysis identifies novel ferroptosis-related biomarkers and therapeutic targets in pulmonary arterial hypertension.

BACKGROUND: Ferroptosis plays a significant role in pulmonary arterial hypertension (PAH), although its underlying mechanisms and key pathogenic genes remain unclear. METHODS: Transcriptomic data from human PAH and control lung tissue were obtained from the Gene Expression Omnibus (GEO) database, whereas ferroptosis-related genes (FRGs) were sourced from the MsigDb and FerrDb databases. Differentially expressed FRGs (DE-FRGs) were identified through the intersection of FRGs with differentially expressed genes (DEGs). Functional enrichment analysis was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Key hub genes were identified through Least Absolute Shrinkage and Selection Operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and weighted correlation network analysis (WGCNA). Gene set enrichment analysis (GSEA) was conducted to explore the functional roles and associated pathways of hub genes. The relationship between hub genes and immune infiltration was investigated. Expression levels of potential biomarkers were validated via Quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) in two PAH animal models (monocrotaline-induced and Sugen5416 plus hypoxia-induced PAH). Finally, molecular docking was employed to screen potential therapeutic compounds. RESULTS: A total of 133 DE-FRGs were identified, with KEGG and GO analyses highlighting their involvement in intracellular iron homeostasis and ferroptosis. Hub genes, notably FZD7 and NFE2, were identified using LASSO, SVM-RFE, and WGCNA. Immune infiltration analysis suggested that monocytes and neutrophils play key roles in PAH pathogenesis. Validation in PAH animal models showed significant upregulation of Fzd7 and downregulation of Nfe2 in lung tissues of both MCT- and SuHx-induced PAH models. Molecular docking identified tetrachlorodibenzodioxin (TCDD) has good binding affinity. CONCLUSION: In summary, we investigated two ferroptosis-related biomarkers, FZD7 and NFE2, in PAH using transcriptomics, offering new insights into molecular mechanisms and potential targeted therapies for the disease.

Ferroptosis↗

PubMed2024

Analysis of different expression RNA binding protein genes in mouse microglia cell from the brains of mice 72 h after subarachnoid hemorrhage or sham operation.

BACKGROUND: The prognosis of brain injury caused by subarachnoid hemorrhage (SAH) is poor. Previous studies showed that abnormal function of RBPs might be involved in brain injury, neuroinflammation and further affect microglia homeostasis. However, no studies have systematically analyzed the genome-wide abnormal expression of RBPs genes in microglia during SAH. METHODS: RNA-seq data of microglia from the SAH mouse group (SAH) and control sham-operated mouse group (sham) were downloaded from the GEO database in GSE167957, including four samples from the sham group and four samples from the SAH group for subsequent analysis.Utilizing GO and KEGG functional enrichment analyses, we conducted a comprehensive study of differentially expressed genes (DEGs), alternative splicing patterns, and co-expression networks to gain deeper insights into the differential expression of RNA-binding proteins (RBPs) and differential alternative splicing events (ASEs) between the SAH (subarachnoid hemorrhage) and sham groups. This analysis aimed to elucidate the potential mechanisms underlying the aberrant expression of RBPs in microglia during brain injury caused by SAH. RESULTS: ASEs and co-expression analyses of differentially expressed RBPs and differential ASEs were carried out in microglia in terms of gene expression. GO and KEGG functional enrichment analysis showed that aberrantly expressed RBPs such as Mcm7, Mtdh, SRSF3, and Hnrnpa2b1 may affect and regulate downstream Csnk1d, Uckl1 and other protein phosphorylation-related genes by alterative splicing. CONCLUSION: RBPs were aberrantly expressed in microglia during the development of brain injury secondary to SAH, regulating alterative splicing of downstream genes and influencing the progression of SAH brain injury in this study. This implies that RBPs are important for the identification of new therapeutic targets for brain injury after SAH.

Animals↗

PubMed2022

Krüppel-like factor 5 promotes the progression of oral squamous cell carcinoma via the baculoviral IAP repeat containing 5 gene.

BACKGROUND: Krüppel-like factor 5 (KLF5) is highly expressed in a variety of tumors, and our study aimed to investigate the role of KLF5 in oral squamous cell carcinoma (OSCC). METHODS: To explore the differential expression of KLF5, next-generation sequencing (NGS) and further analyses were conducted in paired premalignant and tumor tissues and adjacent normal mucosa. We then analyzed the mRNA expression data from The Cancer Genome Atlas (TCGA) and performed gene set enrichment analysis (GSEA) to predict the function of KLF5. Small interfering RNA (siRNA) targeting KLF5 was used to knock down its expression in cells and further evaluate the changes in cell apoptosis, proliferation, and migration. We predicted whether baculoviral inhibitor of apoptosis protein (IAP) repeat containing 5 (BIRC5) was the potential target gene of KLF5 via the NCBI and JASPAR databases. Furthermore, we analyzed BIRC5 expression after KLF5 knockdown and explored its function in athymic BALB/c nude mice. RESULTS: KLF5 expression in clinical samples gradually increased from normal mucosa tissues to premalignant and then to OSCC tissues. Analysis of TCGA data and GSEA also suggested that KLF5 was expressed at higher levels in OSCC and involved apoptosis and the protein 53 (P53), transforming growth factor-β (TGF-β), and wingless/integrated (Wnt) signaling pathways. Cell apoptosis was promoted, whereas proliferation and migration were inhibited after KLF5 knockdown. Furthermore, we found KLF5 transcription binding sites on the BIRC5 promoter and BIRC5 expression was inhibited after suppressing KLF5 in vitro and in vivo. CONCLUSIONS: Our findings indicate that KLF5 promotes the development of OSCC via BIRC5, and could be a potential diagnostic and therapeutic target for OSCC.

Krüppel-like factor 5 (KLF5)↗

PubMed2026

Identification of novel HUWE1 variants in Turner-type X-linked intellectual disability.

OBJECTIVE: To characterize the clinical phenotypes and identify the genetic etiology in four unrelated families affected by Turner-type X-linked intellectual disability (XLID). METHODS: Peripheral blood samples were collected from four probands and their parents. Genomic DNA was extracted, and a comprehensive genetic analysis was performed using trio-based Whole Exome Sequencing (WES) combined with low-pass Copy Number Variation sequencing (CNV-seq). Candidate variants were subsequently validated via Sanger sequencing. RESULTS: Genetic analysis identified distinct variants in the HUWE1 across the four families. Specifically, four distinct HUWE1 variants were identified across the families: a hemizygous c.10034 > T (p.Lys3345Met) in Family 1; a heterozygous c.9209G > A (p.Arg3070His) in Family 2; a heterozygous c.12688T > C (p.Phe4230Leu) in Family 3; and a hemizygous c.9070G > A (p.Ala3024Thr) in Family 4. In accordance with ACMG guidelines, the novel variants in Families 1, 3, and 4 were classified as "Likely Pathogenic" (PS2 + PM2_Supporting + PP2 + PP3). In contrast, the previously reported variant in Family 2 was categorized as "Pathogenic" based on the criteria PS2 + PM2_Supporting + PM5 + PP2 + PP3_Moderate. All probands were clinically diagnosed with Turner-type XLID. CONCLUSIONS: This study expands the pathogenic variant spectrum of HUWE1 and provides novel molecular evidence for the clinical diagnosis of Turner-type XLID. These findings are of significant value for genetic counseling, carrier screening, and prenatal diagnosis for the affected families.

Humans↗

PubMed2024

Deciphering the molecular nexus of BTG2 in periodontitis and diabetic kidney disease.

OBJECTIVE: To investigate the role of BTG2 in periodontitis and diabetic kidney disease (DKD) and its potential underlying mechanism. METHODS: Gene expression data for periodontitis and DKD were acquired from the Gene Expression Omnibus (GEO) database. Differential expression analysis identified co-expressed genes between these conditions. The Nephroseq V5 online nephropathy database validated the role of these genes in DKD. Pearson correlation analysis identified genes associated with our target gene. We employed Gene Set Enrichment Analysis (GSEA) and Protein-Protein Interaction (PPI) networks to elucidate potential mechanisms. Expression levels of BTG2 mRNA were examined using quantitative polymerase Chain Reaction (qPCR) and immunofluorescence assays. Western blotting quantified proteins involved in epithelial-to-mesenchymal transition (EMT), apoptosis, mTORC1 signaling, and autophagy. Additionally, wound healing and flow cytometric apoptosis assays evaluated podocyte migration and apoptosis, respectively. RESULTS: Analysis of GEO database data revealed BTG2 as a commonly differentially expressed gene in both DKD and periodontitis. BTG2 expression was reduced in DKD compared to normal conditions and correlated with proteinuria. GSEA indicated enrichment of BTG2 in the EMT and mTORC1 signaling pathways. The PPI network highlighted BTG2's relevance to S100A9, S100A12, and FPR1. Immunofluorescence assays demonstrated significantly lower BTG2 expression in podocytes under high glucose (HG) conditions. Reduced BTG2 expression in HG-treated podocytes led to increased levels of EMT markers (α-SMA, vimentin) and the apoptotic protein Bim, alongside a decrease in nephrin. Lower BTG2 levels were associated with increased podocyte mobility and apoptosis, as well as elevated RPS6KB1 and mTOR levels, but reduced autophagy marker LC3. CONCLUSION: Our findings suggest that BTG2 is a crucial intermediary gene linking DKD and periodontitis. Modulating autophagy via inhibition of the mTORC1 signaling pathway, and consequently suppressing EMT, may be pivotal in the interplay between periodontitis and DKD.

Periodontitis↗

PubMed2005

Molecular cloning and characterization of two novel truncated isoforms of human Na+/Ca2+ exchanger 3, expressed in fetal brain.

The human gene encoding the Na+/Ca2+ exchanger family member 3 (NCX3) undergoes extensive alternative splicing, with four variants previously identified. In this study, we report two novel alternative transcripts encoding two N-terminally truncated NCX3 proteins specifically expressed in human fetal brain. The identified transcripts, designated NCX3-tN.1 and NCX3-tN.2, are approximately 2.8 kb and 2.9 kb, respectively. The open reading frames (ORFs) are predicted to encode separately a 284 and a 298 amino acid (aa) polypeptide. Sequence analysis and bioinformatics reveal that NCX3-tN.1 and NCX3-tN.2 are the result of alternative splicing of the NCX3 gene. They have their own potential start codons and unique 5' untranslated regions (UTRs) that are different from those of the known NCX3 variants. The variants include a part of intron 2 of the original gene organization as their first exon (exon "a") at the 5' end of the novel transcripts. NCX3-tN.2 consists of six exons including exon "a" and exons 4, 6, 7, 8 and 9 of NCX3, while NCX3-tN.1 lacks exon 4, but is otherwise similar to NCX3-tN.2. Expression studies show that both variants can be translated into protein and NCX3-tN.1 seems more efficiently translated. Based on their structural features, NCX3-tN.1 and NCX3-tN.2 proteins are potentially involved in regulation of Na+/Ca2+ homeostasis.

Adult↗

PubMed2026

MRI-based radiomics model for predicting VEGFA expression and prognosis in lower-grade glioma.

BACKGROUND: Gliomas are the most common primary tumors of the central nervous system. Their treatment remains highly challenging, with high rates of associated disability and mortality. Conventional prognostic indicators no longer adequately satisfy the clinical demands of precision medicine. Therefore, it is essential to further explore novel prognostic biomarkers to enable accurate risk stratification and to provide new reference indicators for personalized precision therapy. PURPOSES: This study aimed to investigate the prognostic significance of vascular endothelial growth factor A (VEGFA) in patients diag nosed with lower-grade gliomas (LGGs) using an MRI based radiomics model. METHODS: Data regarding VEGFA expression and clinical records of LGG patients were retrieved from The Cancer Genome Atlas (TCGA). Corresponding preoperative MRI data were obtained from The Cancer Imaging Archive (TCIA) for radiomic feature extraction. Patients were stratified into high- and low- VEGFA expression groups based on survival information from the current cohort using the survminer package. The overall survival (OS) was assessed using Kaplan-Meier analysis and Cox proportional hazards regression. Predictive models were developed using logistic regression (LR), and model performance was evaluated via receiver operating characteristic (ROC) curve analysis, with area under the curve (AUC) values reported. An optimized model incorporating the Akaike information criterion (AIC) was also constructed (AIC-LR). RESULTS: VEGFA expression was significantly associated with OS (P = 0.002). Multivariate Cox regression confirmed VEGFA as an independent prognostic factor (hazard ratio [HR] = 2.545, 95% confidence interval: 1.422-4.555). Furthermore, VEGFA expression correlated with immune infiltration levels, particularly of M1 and M2 macrophages and T follicular helper cells, and was associated with enrichment in Wnt signaling and B cell receptor signaling pathways. The LR and AIC-LR models demonstrated acceptable predictive performance, with AUCs of 0.728 (95% CI: 0.612-0.843) and 0.725(95% CI: 0.612-0.839) in the training cohort, and 0.704 (95% CI: 0.562-0.847) and 0.718(95% CI: 0.576-0.861) in the validation cohort, respectively. CONCLUSIONS: The MRI based radiomics model showed potential for noninvasive assessment of VEGFA expression and may provide auxiliary information for prognostic evaluation in LGG. Further validation in larger samples and independent external cohorts is required before clinical application.

Radiomics↗

PubMed2005

Genome-wide identification of potential plant E2F target genes.

Entry into the S phase of the cell cycle is controlled by E2F transcription factors that induce the transcription of genes required for cell cycle progression and DNA replication. Although the E2F pathway is highly conserved in higher eukaryotes, only a few E2F target genes have been experimentally validated in plants. We have combined microarray analysis and bioinformatics tools to identify plant E2F-responsive genes. Promoter regions of genes that were induced at the transcriptional level in Arabidopsis (Arabidopsis thaliana) seedlings ectopically expressing genes for the E2Fa and DPa transcription factors were searched for the presence of E2F-binding sites, resulting in the identification of 181 putative E2F target genes. In most cases, the E2F-binding element was located close to the transcription start site, but occasionally could also be localized in the 5' untranslated region. Comparison of our results with available microarray data sets from synchronized cell suspensions revealed that the E2F target genes were expressed almost exclusively during G1 and S phases and activated upon reentry of quiescent cells into the cell cycle. To test the robustness of the data for the Arabidopsis E2F target genes, we also searched for the presence of E2F-cis-acting elements in the promoters of the putative orthologous rice (Oryza sativa) genes. Using this approach, we identified 70 potential conserved plant E2F target genes. These genes encode proteins involved in cell cycle regulation, DNA replication, and chromatin dynamics. In addition, we identified several genes for potentially novel S phase regulatory proteins.

Arabidopsis↗

PubMed2003

Statistical bioinformatic methods in microbial genome analysis.

It is probable that, increasingly, genome investigations are going to be based on statistical formalization. This review summarizes the state of art and potentiality of using statistics in microbial genome analysis. First, I focus on recent advances in functional genomics, such as finding genes and operons, identifying gene conversion events, detecting DNA replication origins and analysing regulatory sites. Then I describe how to use phylogenetic methods in genome analysis and methods for genome-wide scanning for positively selected amino acids. I conclude with speculations on the future course of genome statistical modeling.

Computational Biology↗

PubMed2004

RELIC--a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites.

Phage display technology provides a versatile tool for exploring the interactions between proteins, peptides and small molecule ligands. Quantitative analysis of peptide population sequence diversity and bias patterns has the power to significantly enhance the impact of these methods [1, 2]. We have developed a suite of computational tools for the analysis of peptide populations and made them accessible by integrating fifteen software programs for the analysis of combinatorial peptide sequences into the REceptor LIgand Contacts (RELIC) relational database and web-server. These programs have been developed for the analysis of statistical properties of peptide populations; identification of weak consensus sequences within these populations; and the comparison of these peptide sequences to those of naturally occurring proteins. RELIC is particularly suited to the analysis of peptide populations affinity selected with a small molecule ligand such as a drug or metabolite. Within this functional context, the ability to identify potential small molecule binding proteins using combinatorial peptide screening will accelerate as more ligands are screened and more genome sequences become available. The broader impact of this work is the addition of a novel means of analyzing peptide populations to the phage display community.

Algorithms↗

PubMed2003

Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome.

In order to discover novel protein markers indicative of disease processes or drug effects, the proteomics technology platform most commonly used consists of high resolution protein separation by two-dimensional electrophoresis (2-DE), mass spectrometric identification of proteins from stained gel spots and a bioinformatic data analysis process supported by statistics. This approach has been more successful in profiling proteins and their disease- or treatment-related quantitative changes in tissue homogenates than in plasma samples. Plasma protein display and quantitation suffer from several disadvantages: very high abundance of a few proteins; high heterogeneity of many proteins resulting in long charge trains; crowding of 2-DE separated protein spots in the molecular mass range between 45-80 kD and in the isoelectric point range between 4.5 and 6. Therefore, proteomic technologies are needed that address these problems and particularly allow accurate quantitation of a larger number of less abundant proteins in plasma and other body fluids. The immunoaffinity-based protein subtraction chromatography (IASC) described here removes multiple proteins present in plasma and serum in high concentrations effectively and reproducibly. Applying IASC as an upfront plasma sample preparation process for 2-DE, the protein spot pattern observed in gels changes dramatically and at least 350 additional lower abundance proteins are visualized. Affinity-purified polyclonal antibodies (pAbs) are the immunoaffinity reagents used to specifically remove the abundant proteins such as albumin, immunoglobulin G, immunoglobulin A, transferrin, haptoglobin, alpha-1-antitrypsin, hemopexin, transthyretin, alpha-2-HS glycoprotein, alpha-1-acid glycoprotein, alpha-2-macroglobulin and fibrinogen from human plasma samples. To render the immunoaffinity subtraction procedure recyclable, the pAbs are immobilized and cross-linked on chromatographic matrices. Antibody-coupled matrices specific for one protein each can be pooled to form mixed-bed IASC columns. We show that up to ten affinity-bound plasma proteins with similar solubility characteristics are eluted from a mixed-bed column in one step. This facilitates automated chromatographic processing of plasma samples in high throughput, which is desirable in proteomic disease marker discovery projects.

Antibodies↗

PubMedDate not supplied

'Genomics': buzzword or reality?

'Genomics' has become a widely used term, covering a range of approaches that make use of the newly acquired wealth of genome data (both on man and on a number of model organisms) to gain new insights and accelerate research. This review attempts to present a clear and balanced view of developments in this field, to describe the four major approaches that contribute to genomics (bioinformatics, genetic analysis of extended populations, large-scale expression studies, functional approaches), and to indicate applications in basic and pharmaceutical research.

Animals↗