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Antibodypedia seeks to answer the question: “How good is that antibody?” Although antibodies are useful reagents, those that work well for immunohistochemistry (IHC) staining may not work well for western blotting or vice versa. Information about such variability often is not reported, so Mathias Uhle´n and Erik Bjo¨rling at AlbaNova University Center (Sweden) developed a resource called Antibodypedia (www.antibodypedia.org) to collect and disseminate this information under the ProteomeBinders banner. The gene-centric portal allows providers of antibodies to share validation data on publicly available antibodies in a standardized way. For every antibody, a provider must submit scores that indicate whether the validation data are “supportive”, “uncertain”, or “nonsupportive” of the antibody’s application to various types of assays, including IHC, western blots, protein arrays, and immunofluorescence staining. In addition, experimental evidence in the form of an image must be provided when the evidence is scored as supportive or uncertain. Information can be entered for single antibodies with the standard form, or for multiple antibodies with an XML data standard. Because validation scores are subjective, all submissions are reviewed before they are posted to the website. Entries are not staticsfeedback from researchers who use the antibodies will be incorporated. Visitors to the website can search the antibodies by the target’s gene name, protein name, or chromosomal location. The search results display links to UniProt and Ensembl entries, the name of the species in which the antibody was generated, a binder ID, and a color-coded validation summary. Clicking on the binder ID takes a researcher to a page with more detailed information, including the target sequence against which the antibody was generated, as well as a link to the provider’s website. All of the antibodies currently in Antibodypedia were submitted by researchers working on the Human
10.1021/pr800626d
2008 American Chemical Society
Protein Atlas (www.proteinatlas.org), but now all researchers who generate antibodies are encouraged to enter information. (Mol. Cell. Proteomics 2008, DOI 10.1074/mcp.M800264MCP200) —Katie Cottingham pr800626d
HUSERMET researchers look to the metabolome for answers Systems biology, the integration of data from various scientific fields to form a comprehensive or “systems” view of an organism, has become a popular pursuit. Over the past 5-10 years, large collaborative research groups have generated vast quantities of data on the genomics, transcriptomics, and proteomics of humans and other organisms. However, Douglas Kell of the University of Manchester (UM) realized that an important piece of the systems biology puzzle has been missings metabolomics. He explains, “The metabolome, being downstream and perhaps closer to the phenotype [than the transcriptome or proteome is], represents the optimal level for understanding and predicting changes in the biology of a complex system” (Curr. Opin. Microbiol. 2004, 7, 296-307; Drug Discov. Today 2006, 11, 1085-1092). Therefore, in 2005, Kell and colleagues at UM, AstraZeneca, and GlaxoSmithKline formed HUSERMET, a project focused on the metabolomics of the serum of “normal” humans and those afflicted with Alzheimer’s disease and ovarian cancer. HUSERMET researchers are involved in three main studies. The goal of one of the studies is to define the normal human serum metabolome (the identities and amounts of the constituents) and understand how it changes with diet, gender, age, and lifestyle. Kell explains that this project also includes an ethnic diversity element. “The goal of the ethnic study is to ascertain and measure the effects of cultural and social environments on the human metabolome,” says Kell. “In addition, there are specific health risks that are
known to be associated with certain groups.” Thus, HUSERMET investigators will use metabolomics to identify risk factors and thereby potentially find ways to obviate the risks. In the Alzheimer’s and ovarian cancer studies, researchers are looking for possible diagnostic markers as well as markers that could predict patients’ responses to therapies or monitor the effectiveness of interventions. Currently, the investigators are preparing several manuscripts on their work in these areas. Collaboration between academic and industrial scientists is an important aspect of HUSERMET. The project is funded by several U.K. organizations through the LINK Applied Genomics Program, which was formed to promote such partnerships after the first draft of the human genome sequence was published. Now closed, this LINK program “has encouraged the exchange of knowledge into industry from the research base and given the research base access to the latest techniques developed by industry to optimize the exploitation of genomics,” explains Kell. Although one might expect such collaborations to be a one-way streetswith industrial researchers holding back datasKell reports that this was not the case for HUSERMET. “We have not encountered any barriers, and the industrial and academic partners have been very open with each other with regard both to data and to best working practices,” he notes. Funding for the project ends in 2009, but the researchers plan to continue their collaborations with funds from other sources. The team will follow some of the cohorts over time and incorporate morbidity and mortality data into the HUSERMET analysis. “The true value of this data set will be over the coming years when health events and outcomes are more fully known for the volunteers,” Kell says. In addition, data mining will continue, and a database of clinical and analytical data and metadata is expected to be publicly available in 2011. The latest information can be found at www.husermet.org. —Katie Cottingham pr8006073
Journal of Proteome Research • Vol. 7, No. 10, 2008 4213
