Gene set analysis: challenges, opportunities, and future research
Gene set analysis methods are widely used to provide insight into high-throughput gene
expression data. There are many gene set analysis methods available. These methods rely …
expression data. There are many gene set analysis methods available. These methods rely …
Identifying significantly impacted pathways: a comprehensive review and assessment
Background Many high-throughput experiments compare two phenotypes such as disease
vs. healthy, with the goal of understanding the underlying biological phenomena …
vs. healthy, with the goal of understanding the underlying biological phenomena …
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods
Gene set analysis (GSA) is used to elucidate genome-wide data, in particular transcriptome
data. A multitude of methods have been proposed for this step of the analysis, and many of …
data. A multitude of methods have been proposed for this step of the analysis, and many of …
Ten years of pathway analysis: current approaches and outstanding challenges
Pathway analysis has become the first choice for gaining insight into the underlying biology
of differentially expressed genes and proteins, as it reduces complexity and has increased …
of differentially expressed genes and proteins, as it reduces complexity and has increased …
Pathway analysis: state of the art
MA García-Campos, J Espinal-Enríquez… - Frontiers in …, 2015 - frontiersin.org
Pathway analysis is a set of widely used tools for research in life sciences intended to give
meaning to high-throughput biological data. The methodology of these tools settles in the …
meaning to high-throughput biological data. The methodology of these tools settles in the …
A general modular framework for gene set enrichment analysis
M Ackermann, K Strimmer - BMC bioinformatics, 2009 - Springer
Background Analysis of microarray and other high-throughput data on the basis of gene
sets, rather than individual genes, is becoming more important in genomic studies …
sets, rather than individual genes, is becoming more important in genomic studies …
Gene set enrichment analysis: performance evaluation and usage guidelines
A central goal of biology is understanding and describing the molecular basis of plasticity:
the sets of genes that are combinatorially selected by exogenous and endogenous …
the sets of genes that are combinatorially selected by exogenous and endogenous …
Gene-set approach for expression pattern analysis
D Nam, SY Kim - Briefings in bioinformatics, 2008 - academic.oup.com
Recently developed gene set analysis methods evaluate differential expression patterns of
gene groups instead of those of individual genes. This approach especially targets gene …
gene groups instead of those of individual genes. This approach especially targets gene …
[PDF][PDF] αB‐crystallin complexes with 14‐3‐3ζ to induce epithelial‐mesenchymal transition and resistance to sorafenib in hepatocellular carcinoma
The overall survival of patients with hepatocellular carcinoma (HCC) remains poor, and the
molecular pathogenesis remains incompletely defined in HCC. Here we report that …
molecular pathogenesis remains incompletely defined in HCC. Here we report that …
Gene set analysis methods: statistical models and methodological differences
H Maciejewski - Briefings in bioinformatics, 2014 - academic.oup.com
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 …
empirically in a number of comprehensive review articles. Although it is recognized that …