Identifying significantly impacted pathways: a comprehensive review and assessment

TM Nguyen, A Shafi, T Nguyen, S Draghici - Genome biology, 2019 - Springer
Background Many high-throughput experiments compare two phenotypes such as disease
vs. healthy, with the goal of understanding the underlying biological phenomena …

Ten years of pathway analysis: current approaches and outstanding challenges

P Khatri, M Sirota, AJ Butte - PLoS computational biology, 2012 - journals.plos.org
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 …

Comprehensive molecular characterization of papillary renal-cell carcinoma

Cancer Genome Atlas Research … - New England Journal of …, 2016 - Mass Medical Soc
Background Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell
carcinomas, is a heterogeneous disease that consists of various types of renal cancer …

REVIGO summarizes and visualizes long lists of gene ontology terms

F Supek, M Bošnjak, N Škunca, T Šmuc - PloS one, 2011 - journals.plos.org
Outcomes of high-throughput biological experiments are typically interpreted by statistical
testing for enriched gene functional categories defined by the Gene Ontology (GO). The …

Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly

ER Horton, A Byron, JA Askari, DHJ Ng… - Nature cell …, 2015 - nature.com
Integrin receptor activation initiates the formation of integrin adhesion complexes (IACs) at
the cell membrane that transduce adhesion-dependent signals to control a multitude of …

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

DW Huang, BT Sherman, RA Lempicki - Nature protocols, 2009 - nature.com
DAVID bioinformatics resources consists of an integrated biological knowledgebase and
analytic tools aimed at systematically extracting biological meaning from large gene/protein …

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 …

Cellular and molecular mechanisms of fibrosis

TA Wynn - The Journal of Pathology: A Journal of the …, 2008 - Wiley Online Library
Fibrosis is defined by the overgrowth, hardening, and/or scarring of various tissues and is
attributed to excess deposition of extracellular matrix components including collagen …

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists

DW Huang, BT Sherman, Q Tan, JR Collins, WG Alvord… - Genome biology, 2007 - Springer
Abstract The DAVID Gene Functional Classification Tool http://david. abcc. ncifcrf. gov uses
a novel agglomeration algorithm to condense a list of genes or associated biological terms …

DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists

DW Huang, BT Sherman, Q Tan, J Kir, D Liu… - Nucleic acids …, 2007 - academic.oup.com
All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of
large lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics …