Gene set analysis methods: a systematic comparison
نویسندگان
چکیده
منابع مشابه
Comprehensive Comparison of Gene Set Analysis Tools
Gene set analysis has enhanced the microarray data analysis field with biological insights. The first introduced and widely used Over-representation analysis (ORA) method, has the limitation of the requirement of a predetermined differentially expressed genes list. To overcome this limitation, distribution based analysis (DBA) methods were developed with different analysis steps and null hypoth...
متن کاملA Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity
Identification of functional sets of genes associated with conditions of interest from omics data was first reported in 1999, and since, a plethora of enrichment methods were published for systematic analysis of gene sets collections including Gene Ontology and biological pathways. Despite their widespread usage in reducing the complexity of omics experiment results, their performance is poorly...
متن کاملComparison of Biclustering Methods: A Systematic Comparison and Evaluation of Biclustering Methods for Gene Expression Data
Motivation: In recent years, there have been various efforts to overcome the limitations of standard clustering approaches for the analysis of gene expression data by grouping genes and samples simultaneously. The underlying concept, which is often referred to as biclustering, allows to identify sets of genes sharing compatible expression patterns across subsets of samples, and its usefulness h...
متن کاملGene set analysis methods: statistical models and methodological differences
Many methods of gene set analysis developed in recent years have been compared empirically in a number of comprehensive review articles. Although it is recognized that different methods tend to identify different gene sets as significant, no consensus has been worked out as to which method is preferable, as the recommendations are often contradictory. In this article, we want to group and compa...
متن کاملGene set analysis methods applied to chicken microarray expression data
BACKGROUND Gene set analysis is considered to be a way of improving our biological interpretation of the observed expression patterns. This paper describes different methods applied to analyse expression data from a chicken DNA microarray dataset. RESULTS Applying different gene set analyses to the chicken expression data led to different ranking of the Gene Ontology terms tested. A method fo...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: BioData Mining
سال: 2018
ISSN: 1756-0381
DOI: 10.1186/s13040-018-0166-8