title: Preimplantation development regulatory pathway construction through a text-mining approach.
abstract: BACKGROUND
  The integration of sequencing and gene interaction data and subsequent generation of pathways and networks contained in databases such as KEGG Pathway is essential for the comprehension of complex biological processes. We noticed the absence of a chart or pathway describing the well-studied preimplantation development stages; furthermore, not all genes involved in the process have entries in KEGG Orthology, important information for knowledge application with relation to other organisms.
  
  
  RESULTS
  In this work we sought to develop the regulatory pathway for the preimplantation development stage using text-mining tools such as Medline Ranker and PESCADOR to reveal biointeractions among the genes involved in this process. The genes present in the resulting pathway were also used as seeds for software developed by our group called SeedServer to create clusters of homologous genes. These homologues allowed the determination of the last common ancestor for each gene and revealed that the preimplantation development pathway consists of a conserved ancient core of genes with the addition of modern elements.
  
  
  CONCLUSIONS
  The generation of regulatory pathways through text-mining tools allows the integration of data generated by several studies for a more complete visualization of complex biological processes. Using the genes in this pathway as "seeds" for the generation of clusters of homologues, the pathway can be visualized for other organisms. The clustering of homologous genes together with determination of the ancestry leads to a better understanding of the evolution of such process.
authors.affiliation: Laboratório Biodados, Dept. de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte - MG, Brazil.
authors.forename: Elisa
authors.initials: E
authors.lastname: Donnard
authors.forename: Adriano
authors.initials: A
authors.lastname: Barbosa-Silva
authors.forename: Rafael L M
authors.initials: RL
authors.lastname: Guedes
authors.forename: Gabriel R
authors.initials: GR
authors.lastname: Fernandes
authors.forename: Henrique
authors.initials: H
authors.lastname: Velloso
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Kohn
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade-Navarro
authors.forename: J Miguel
authors.initials: JM
authors.lastname: Ortega
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D057225:Data Mining; D016208:Databases, Factual; D047108:Embryonic Development; D053263:Gene Regulatory Networks; D006801:Humans; D016247:Information Storage and Retrieval; D051379:Mice; D012984:Software; D033581:Stem Cell Transplantation