title: GenMAPP 2: new features and resources for pathway analysis.
abstract: BACKGROUND
  Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses.
  
  
  RESULTS
  To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a new mode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP), and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages.
  
  
  CONCLUSIONS
  GenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.
authors.affiliation: Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA. nsalomonis@gladstone.ucsf.edu <nsalomonis@gladstone.ucsf.edu>
authors.forename: Nathan
authors.initials: N
authors.lastname: Salomonis
authors.forename: Kristina
authors.initials: K
authors.lastname: Hanspers
authors.forename: Alexander C
authors.initials: AC
authors.lastname: Zambon
authors.forename: Karen
authors.initials: K
authors.lastname: Vranizan
authors.forename: Steven C
authors.initials: SC
authors.lastname: Lawlor
authors.forename: Kam D
authors.initials: KD
authors.lastname: Dahlquist
authors.forename: Scott W
authors.initials: SW
authors.lastname: Doniger
authors.forename: Josh
authors.initials: J
authors.lastname: Stuart
authors.forename: Bruce R
authors.initials: BR
authors.lastname: Conklin
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Pico
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D015870:Gene Expression / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome