title: Atlas of signaling for interpretation of microarray experiments.
abstract: Microarray-based expression profiling of living systems is a quick and inexpensive method to obtain insights into the nature of various diseases and phenotypes. A typical microarray profile can yield hundreds or even thousands of differentially expressed genes and finding biologically plausible themes or regulatory mechanisms underlying these changes is a non-trivial and daunting task. We describe a novel approach for systems-level interpretation of microarray expression data using a manually constructed "overview" pathway depicting the main cellular signaling channels (Atlas of Signaling). Currently, the developed pathway focuses on signal transduction from surface receptors to transcription factors and further transcriptional regulation of cellular "workhorse" proteins. We show how the constructed Atlas of Signaling in combination with an enrichment analysis algorithm allows quick identification and visualization of the main signaling cascades and cellular processes affected in a gene expression profiling experiment. We validate our approach using several publicly available gene expression datasets.
authors.affiliation: Ariadne Genomics, Inc., Rockville, Maryland, United States of America.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Kotelnikova
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanikova
authors.forename: Andrey
authors.initials: A
authors.lastname: Kalinin
authors.forename: Anton
authors.initials: A
authors.lastname: Yuryev
authors.forename: Nikolai
authors.initials: N
authors.lastname: Daraselia
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020543:Proteome / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics*; D012984:Software
chemical_list: D020543:Proteome