Pathway analysis of genomic data: concepts, methods, and prospects for future development
Genome-wide data sets are increasingly being used to identify biological pathways and
networks underlying complex diseases. In particular, analyzing genomic data through sets …
networks underlying complex diseases. In particular, analyzing genomic data through sets …
A review of multivariate analyses in imaging genetics
J Liu, VD Calhoun - Frontiers in neuroinformatics, 2014 - frontiersin.org
Recent advances in neuroimaging technology and molecular genetics provide the unique
opportunity to investigate genetic influence on the variation of brain attributes. Since the year …
opportunity to investigate genetic influence on the variation of brain attributes. Since the year …
Functional characterization of somatic mutations in cancer using network-based inference of protein activity
Identifying the multiple dysregulated oncoproteins that contribute to tumorigenesis in a given
patient is crucial for developing personalized treatment plans. However, accurate inference …
patient is crucial for developing personalized treatment plans. However, accurate inference …
Causal analysis approaches in ingenuity pathway analysis
Motivation: Prior biological knowledge greatly facilitates the meaningful interpretation of
gene-expression data. Causal networks constructed from individual relationships curated …
gene-expression data. Causal networks constructed from individual relationships curated …
Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations
Enrichment analysis of gene sets is a popular approach that provides a functional
interpretation of genome-wide expression data. Existing tests are affected by inter-gene …
interpretation of genome-wide expression data. Existing tests are affected by inter-gene …
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms
Motivation Analysis of gene set (GS) enrichment is an essential part of functional omics
studies. Here, we complement the established evaluation metrics of GS enrichment …
studies. Here, we complement the established evaluation metrics of GS enrichment …
Toward a gold standard for benchmarking gene set enrichment analysis
L Geistlinger, G Csaba, M Santarelli… - Briefings in …, 2021 - academic.oup.com
Motivation Although gene set enrichment analysis has become an integral part of high-
throughput gene expression data analysis, the assessment of enrichment methods remains …
throughput gene expression data analysis, the assessment of enrichment methods remains …
[HTML][HTML] Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer
Y Cheng, D Bu, Q Zhang, R Sun, S Lyle, G Zhao… - Journal of advanced …, 2023 - Elsevier
Introduction Gastric cancer (GC) is the third leading cause of cancer-related deaths in China
and immunotherapy emerging as a revolutionary treatment for GC recently. Tumor …
and immunotherapy emerging as a revolutionary treatment for GC recently. Tumor …
Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA)
Background Our objective was to develop a consistent molecular definition of psoriasis.
There have been several published microarray studies of psoriasis, and we compared …
There have been several published microarray studies of psoriasis, and we compared …
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
Background Gene-set enrichment analyses (GEA or GSEA) are commonly used for
biological characterization of an experimental gene-set. This is done by finding known …
biological characterization of an experimental gene-set. This is done by finding known …