title: Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.
abstract: BACKGROUND
  Genome-wide measurement of transcript levels is an ubiquitous tool in biomedical research. As experimental data continues to be deposited in public databases, it is becoming important to develop search engines that enable the retrieval of relevant studies given a query study. While retrieval systems based on meta-data already exist, data-driven approaches that retrieve studies based on similarities in the expression data itself have a greater potential of uncovering novel biological insights.
  
  
  RESULTS
  We propose an information retrieval method based on differential expression. Our method deals with arbitrary experimental designs and performs competitively with alternative approaches, while making the search results interpretable in terms of differential expression patterns. We show that our model yields meaningful connections between biological conditions from different studies. Finally, we validate a previously unknown connection between malignant pleural mesothelioma and SIM2s suggested by our method, via real-time polymerase chain reaction in an independent set of mesothelioma samples.
  
  
  BACKGROUND
  Supplementary data and source code are available from http://www.ebi.ac.uk/fg/research/rex.
authors: Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland.
authors: José
authors: J
authors: Caldas
authors: Nils
authors: N
authors: Gehlenborg
authors: Eeva
authors: E
authors: Kettunen
authors: Ali
authors: A
authors: Faisal
authors: Mikko
authors: M
authors: Rönty
authors: Andrew G
authors: AG
authors: Nicholson
authors: Sakari
authors: S
authors: Knuutila
authors: Alvis
authors: A
authors: Brazma
authors: Samuel
authors: S
authors: Kaski
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D008654:Mesothelioma / Q000235:genetics*; D051379:Mice; D010997:Pleural Neoplasms / Q000235:genetics*; D011381:Programming Languages; D051381:Rats