Exploring trafficking GTPase function by mRNA expression profiling: use of the SymAtlas web-application and the Membrome datasets.
Despite complete sequencing of the human and mouse genomes, functional annotation of novel gene function still remains a major challenge in mammalian biology. Emerging strategies to help elucidate unknown gene function include the analysis of tissue-specific patterns of mRNA expression. A recent study investigated the steady-state mRNA expression profiling of the vast majority of protein-encoding human and mouse genes across a panel of 79 human and 61 mouse nonredundant tissues. The microarray data from this study constitutes the Genomics Institute of Novartis Foundation (GNF) Human and Mouse Gene Atlases and is publicly available for exploration through the SymAtlas web-application (http://symatlas.gnf.org/). We have recently reported the use of these data and hierarchical clustering algorithms to generate a global overview of the distribution of Rabs, SNAREs, and coat machinery components, as well as their respective adaptors, effectors, and regulators. This systems biology approach led us to propose Rab-centric protein activity hubs as a framework for an integrated coding system, the membrome network, which orchestrates the dynamics of specialized membrane architecture of differentiated cells. Here, we describe the use of the SymAtlas web-application and the Membrome datasets to help explore trafficking GTPase function. The human and mouse membrome datasets are available through the Membrome homepage (http://www.membrome.org/) and correspond to subsets of the SymAtlas content restricted to known membrane trafficking components. Considering the fragmentary nature of the current reductionist approaches in elucidating trafficking component functions, the membrome datasets provide a more focused systems biology perspective that not only complements our current understanding of transport in complex tissues but also provides an integrated perspective of Rab activity in controlling membrane architecture.
Cemal
C
Gurkan
Hilmar
H
Lapp
John B
JB
Hogenesch
William E
WE
Balch
D000818:Animals; D030541:Databases, Genetic; D020558:GTP Phosphohydrolases / Q000378:metabolism*; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D012333:RNA, Messenger / Q000235:genetics*
D012333:RNA, Messenger; D020558:GTP Phosphohydrolases