AI Article Synopsis
- DNA microarrays, or gene chips, provide a comprehensive method for surveying gene expression, revealing which genes are active in a cell or tissue through an expression profile.
- These expression profiles help identify gene involvement in diseases and can be analyzed further using bioinformatics tools to answer complex biological questions.
- The review also covers the creation of microarrays, data management, and their specific applications in renal research and future clinical practices.
Article Abstract
DNA microarrays, or gene chips, allow surveys of gene expression, (i.e., mRNA expression) in a highly parallel and comprehensive manner. The pattern of gene expression produced, known as the expression profile, depicts the subset of gene transcripts expressed in a cell or tissue. At its most fundamental level, the expression profile can address qualitatively which genes are expressed in disease states. However, with the aid of bioinformatics tools such as cluster analysis, self-organizing maps, and principle component analysis, more sophisticated questions can be answered. Microarrays can be used to characterize the functions of novel genes, identify genes in a biologic pathway, analyze genetic variation, and identify therapeutic drug targets. Moreover, the expression profile can be used as a tissue or disease "fingerprint." This review details the fabrication of arrays, data management tools, and applications of microarrays to the field of renal research and the future of clinical practice.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1681/ASN.V1251072 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Classification-based pathway analysis using GPNet with novel P-value computation.
Brief Bioinform
November 2024
Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, United States.
Pathway analysis plays a critical role in bioinformatics, enabling researchers to identify biological pathways associated with various conditions by analyzing gene expression data. However, the rise of large, multi-center datasets has highlighted limitations in traditional methods like Over-Representation Analysis (ORA) and Functional Class Scoring (FCS), which struggle with low signal-to-noise ratios (SNR) and large sample sizes. To tackle these challenges, we use a deep learning-based classification method, Gene PointNet, and a novel $P$-value computation approach leveraging the confusion matrix to address pathway analysis tasks.
View Article and Find Full Text PDFTargeting AXL inhibits the growth and metastasis of prostate cancer in bone.
Clin Cancer Res
January 2025
Stanford University, Palo Alto, CA, United States.
Purpose: After failing primary and secondary hormonal therapy, castration-resistant and neuroendocrine prostate cancer metastatic to the bone is invariably lethal, although treatment with docetaxel and carboplatin can modestly improve survival. Therefore, agents targeting biologically relevant pathways in PCa and potentially synergizing with docetaxel and carboplatin in inhibiting bone metastasis growth are urgently needed.
Experimental Design: Phosphorylated (activated) AXL expression in human prostate cancer bone metastases was assessed by immunohistochemical staining.
Organ-specific microenvironments drive divergent T cell evolution in acute graft-versus-host disease.
Sci Transl Med
January 2025
Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.
Tissue-specific T cell immune responses play a critical role in maintaining organ health but can also drive immune pathology during both autoimmunity and alloimmunity. The mechanisms controlling intratissue T cell programming remain unclear. Here, we leveraged a nonhuman primate model of acute graft-versus-host disease (aGVHD) after allogeneic hematopoietic stem cell transplantation to probe the biological underpinnings of tissue-specific alloimmune disease using a comprehensive systems immunology approach including multiparameter flow cytometry, population-based transcriptional profiling, and multiplexed single-cell RNA sequencing and TCR sequencing.
View Article and Find Full Text PDFPrior vaccination prevents overactivation of innate immune responses during COVID-19 breakthrough infection.
Sci Transl Med
January 2025
Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
At this stage in the COVID-19 pandemic, most infections are "breakthrough" infections that occur in individuals with prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure. To refine long-term vaccine strategies against emerging variants, we examined both innate and adaptive immunity in breakthrough infections. We performed single-cell transcriptomic, proteomic, and functional profiling of primary and breakthrough infections to compare immune responses from unvaccinated and vaccinated individuals during the SARS-CoV-2 Delta wave.
View Article and Find Full Text PDFComparative analysis of antibiotic resistance genes between fresh pig manure and composted pig manure in winter, China.
PLoS One
January 2025
School of Environmental Engineering, Yellow River Conservancy Technical Institute, Kaifeng Key Laboratory of Food Composition and Quality Assessment, Kaifeng, China.
Antibiotic resistance is a critical global public health issue. The gut microbiome acts as a reservoir for numerous antibiotic resistance genes (ARGs), which influence both existing and future microbial populations within a community or ecosystem. However, the differences in ARG expression between fresh and composted feces remain poorly understood.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!