Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFkappaB and the unfolded protein response in certain B-cell lymphomas.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545785PMC
http://dx.doi.org/10.1186/gb-2004-5-11-r94DOI Listing

Publication Analysis

Top Keywords

consensus clustering
8
clustering functional
4
functional interpretation
4
interpretation gene-expression
4
gene-expression data
4
data microarray
4
microarray analysis
4
analysis clustering
4
clustering algorithms
4
algorithms suffer
4

Similar Publications

A Golgi apparatus‑related subtype and risk signature predicts prognosis and evaluates immunotherapy response in gastric cancer.

Discov Oncol

January 2025

Department of Gastrointestinal Surgery, Yantai Yuhuangding Hospital, Qingdao University, No. 20 Yuhuangding East Road, Zhifu District, Yantai, 264001, China.

Background: Gastric cancer (GC) remains a significant health burden, calling for the discovery of novel biomarkers. Golgi apparatus, a crucial cellular organelle involved in tumorigenesis, remains underexplored in GC research. A comprehensive understanding of its role and associated mechanisms is urgently needed.

View Article and Find Full Text PDF

Identification of pain-related long non-coding RNAs for pulpitis prediction.

Clin Oral Investig

January 2025

Department of Endodontics, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China.

Objectives: We investigated the recently generated RNA-sequencing dataset of pulpitis to identify the potential pain-related lncRNAs for pulpitis prediction.

Materials And Methods: Differential analysis was performed on the gene expression profile between normal and pulpitis samples to obtain pulpitis-related genes. The co-expressed gene modules were identified by weighted gene coexpression network analysis (WGCNA).

View Article and Find Full Text PDF

Background: Synovitis is one of the key pathological feature driving osteoarthritis (OA) development. Diverse programmed cell death (PCD) pathways are closely linked to the pathogenesis of OA, but few studies have explored the relationship between PCD-related genes and synovitis.

Methods: The transcriptome expression profiles of OA synovial samples were obtained from the Gene Expression Omnibus (GEO) database.

View Article and Find Full Text PDF

Background: Sarcopenia, an aseptic chronic inflammatory disease, is a complex and debilitating disease characterized by the progressive degeneration of skeletal muscle. PANoptosis, a novel proinflammatory programmed cell death pathway, has been linked to various diseases. However, the precise role of PANoptosis-related features in sarcopenia remains uncertain.

View Article and Find Full Text PDF

Introduction: Diabetic nephropathy (DN) is a common diabetes-related complication with unclear underlying pathological mechanisms. Although recent studies have linked glycolysis to various pathological states, its role in DN remains largely underexplored.

Methods: In this study, the expression patterns of glycolysis-related genes (GRGs) were first analyzed using the GSE30122, GSE30528, and GSE96804  datasets, followed by an evaluation of the immune landscape in DN.

View Article and Find Full Text PDF

Want 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!