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List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists

The George Washington University Medical Center, Department of Biochemistry and Molecular Biology, 2300 I Street NW. Ross Hall 541, Washington, D.C. 20037, United States.
Gene (Impact Factor: 2.08). 11/2005; 360(1):78-82. DOI: 10.1016/j.gene.2005.07.008
Source: PubMed

ABSTRACT Microarray profiling of RNA expression is a powerful tool that generates large lists of transcripts that are potentially relevant to a disease or treatment. However, because the lists of changed transcripts are embedded in figures and tables, they are typically inaccessible for search engines. Due to differences in gene nomenclatures, the lists are difficult to compare between studies. LOLA (Lists of Lists Annotated) is an internet-based database for comparing gene lists from microarray studies or other genomic-scale methods. It serves as a common platform to compare and reannotate heterogeneous gene lists from different microarray platforms or different genomic methodologies such as serial analysis of gene expression (SAGE) or proteomics. LOLA () provides researchers with a means to store, annotate, and compare gene lists produced from different studies or different analyses of the same study. It is especially useful in identifying potentially "high interest" genes which are reported as significant across multiple studies and species. Its application to the fields of stem cell, cancer, and aging research is demonstrated by comparing published papers.

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    • "A proof-of-concept study by Hughes et al. (2000) demonstrated a general approach for functional annotation of uncharacterized genes and pharmacological perturbations using a reference database of expression profiles corresponding to 300 diverse chemical treatments and mutations in yeast (Hughes et al., 2000). However, despite significant advances in the storage, analysis and mining of microarray data, as well as the development of web-based tools, Cahan et al. (2005, 2007) noted that the resulting differentially expressed gene (DEG) lists were not amenable to electronic access, and remained inaccessible for comparison purposes. The poor consistency in determining DEGs and the uncertainty in selecting calculation methods may account for the observed shortfall. "
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