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 …
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 …
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 …
carcinomas, is a heterogeneous disease that consists of various types of renal cancer …
REVIGO summarizes and visualizes long lists of gene ontology terms
Outcomes of high-throughput biological experiments are typically interpreted by statistical
testing for enriched gene functional categories defined by the Gene Ontology (GO). The …
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
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 …
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 …
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 …
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 …
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 …
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 …
large lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics …