While generation of high-throughput expression data is becoming routine, the fast, easy, and
systematic presentation and analysis of these data in a biological context is still an obstacle …

Background Biochemical pathways provide an essential context for understanding
comprehensive experimental data and the systematic workings of a cell. Therefore, the …

Motivation: Gene expression analysis with microarrays has become one of the most widely
used high-throughput methods for gathering genome-wide functional data. Emerging-omics …

With the integration of the KEGG and Predictome databases as well as two search engines
for coexpressed genes/proteins using data sets obtained from the Stanford Microarray …

Motivation: As the blueprints of cellular actions, biological pathways characterize the roles of
genomic entities in various cellular mechanisms, and as such, their availability, manipulation …

Escher is a web application for visualizing data on biological pathways. Three key features
make Escher a uniquely effective tool for pathway visualization. First, users can rapidly …

Pathway analysis is widely used in omics studies. Pathway-based data integration and
visualization is a critical component of the analysis. To address this need, we recently …

We have developed PathBuilder, an open-source web application to annotate biological
information pertaining to signaling pathways and to create web-based pathway resources …

Background Biological pathways are a useful abstraction of biological concepts, and
software tools to deal with pathway diagrams can help biological research. PathVisio is a …

In this paper, we present KEGGscape a pathway data integration and visualization app for
Cytoscape (http://apps. cytoscape. org/apps/keggscape). KEGG is a comprehensive public …