Creation of gene expression database on preeclampsia-affected human placenta

Abstract

Publication of gene expression raw data in open access at online resources like NCBI or ArrayExpress made it possible to use these data for cross-experiment integrative analysis and make new insights into biological phenomena. However, most popular of the present online resources are meant to be archives rather than ready for immediate access and interpretation databases. Data uploaded by independent contributors is not standardized and sometimes incomplete and needs further processing before it is ready for the analysis. Hence, the need for a specialized database appears.\n\nGiven in this article is the description of the database that was created after processing a collection of 33 relevant datasets on pre-eclampsia-affected human placenta. Data processing includes the choice of relevant experiments from ArrayExpress database, the experiment sample attributes standardization according to MeSH term dictionary and Experimental Factor Ontology and the completion of missing data using information from the corresponding articles and authors.\n\nA database of more than 1000 samples contains sufficient sample-wise metadata for them to be arranged into relevant case-control groups. Metadata includes information on biological specimen, donors diagnosis, gestational age, mode of delivery etc. The average size of these groups will be higher than it is in separate experiments. This will reduce experiment bias and enhance statistical accuracy of the subsequent analysis such as search for differentially expressed genes or inferring gene networks. The article concludes with the guidelines for the microarray experiment metadata uploading for future contributors.