RAMP: a bioinformatics framework for researching imaging agents through molecular pathways.
Signaling pathways are the fundamental grammar of cellular communication, yet few frameworks are available to analyze molecular imaging probes in the context of signaling pathways. Such a framework would aid in the design and selection of imaging probes for measuring specific signaling pathways and, vice versa, help illuminate which pathways are being assayed by a given probe. RAMP (Researching imaging Agents through Molecular Pathways) is a bioinformatics framework for connecting signaling pathways and imaging probes using a controlled vocabulary of the imaging targets. RAMP contains signaling pathway data from MetaCore, the Kyoto Encyclopedia of Genes and Genomes, and the Gene Ontology project; imaging probe data from the Molecular Imaging and Contrast Agent Database (MICAD); and tissue protein expression data from The Human Protein Atlas. The RAMP search tool is available at <http://www.rampsearch.com>. Examples are presented to demonstrate the utility of RAMP for pathway-based searches of molecular imaging probes.
Novartis Institutes for Biomedical Research, Biomarker Development, Cambridge, MA 02139, USA. edward.khokhlovich@novartis.com
Edward
E
Khokhlovich
Daniel
D
Wahl
Anthony
A
Masiello
Pierre
P
Parisot
Stefan
S
El-Ghatta
Joseph D
JD
Szustakowski
Nanguneri
N
Nirmala
David S
DS
Tuch
D019295:Computational Biology / Q000379:methods*; D003287:Contrast Media / Q000737:chemistry* / Q000378:metabolism*; D016208:Databases, Factual; D006801:Humans; D020407:Internet; D008954:Models, Biological; D057054:Molecular Imaging; D011506:Proteins / Q000032:analysis / Q000378:metabolism; D015398:Signal Transduction; D012984:Software
D003287:Contrast Media; D011506:Proteins