[HTML][HTML] 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 …
Big data analytics in healthcare
A Belle, R Thiagarajan… - BioMed research …, 2015 - Wiley Online Library
The rapidly expanding field of big data analytics has started to play a pivotal role in the
evolution of healthcare practices and research. It has provided tools to accumulate, manage …
evolution of healthcare practices and research. It has provided tools to accumulate, manage …
[HTML][HTML] 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 …
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
DW Huang, BT Sherman, RA Lempicki - Nucleic acids research, 2009 - academic.oup.com
Functional analysis of large gene lists, derived in most cases from emerging high-throughput
genomic, proteomic and bioinformatics scanning approaches, is still a challenging and …
genomic, proteomic and bioinformatics scanning approaches, is still a challenging and …
[HTML][HTML] Enrichment map: a network-based method for gene-set enrichment visualization and interpretation
Background Gene-set enrichment analysis is a useful technique to help functionally
characterize large gene lists, such as the results of gene expression experiments. This …
characterize large gene lists, such as the results of gene expression experiments. This …
[HTML][HTML] 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 …
MetPA: a web-based metabolomics tool for pathway analysis and visualization
J Xia, DS Wishart - Bioinformatics, 2010 - academic.oup.com
MetPA (Metabolomics Pathway Analysis) is a user-friendly, web-based tool dedicated to the
analysis and visualization of metabolomic data within the biological context of metabolic …
analysis and visualization of metabolomic data within the biological context of metabolic …
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics
D Tabas-Madrid, R Nogales-Cadenas… - Nucleic acids …, 2012 - academic.oup.com
Since its first release in 2007, GeneCodis has become a valuable tool to functionally
interpret results from experimental techniques in genomics. This web-based application …
interpret results from experimental techniques in genomics. This web-based application …
GO:: TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of …
EI Boyle, S Weng, J Gollub, H Jin, D Botstein… - …, 2004 - academic.oup.com
GO:: TermFinder comprises a set of object-oriented Perl modules for accessing Gene
Ontology (GO) information and evaluating and visualizing the collective annotation of a list of …
Ontology (GO) information and evaluating and visualizing the collective annotation of a list of …
A novel signaling pathway impact analysis
Motivation: Gene expression class comparison studies may identify hundreds or thousands
of genes as differentially expressed (DE) between sample groups. Gaining biological insight …
of genes as differentially expressed (DE) between sample groups. Gaining biological insight …