title: EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer.
abstract: The development of colorectal cancer (CRC)-the third most common cancer type-has been associated with deregulations of cellular mechanisms stimulated by both genetic and epigenetic events. StatEpigen is a manually curated and annotated database, containing information on interdependencies between genetic and epigenetic signals, and specialized currently for CRC research. Although StatEpigen provides a well-developed graphical user interface for information retrieval, advanced queries involving associations between multiple concepts can benefit from more detailed graph representation of the integrated data. This can be achieved by using a graph database (NoSQL) approach. Data were extracted from StatEpigen and imported to our newly developed EpiGeNet, a graph database for storage and querying of conditional relationships between molecular (genetic and epigenetic) events observed at different stages of colorectal oncogenesis. We illustrate the enhanced capability of EpiGeNet for exploration of different queries related to colorectal tumor progression; specifically, we demonstrate the query process for (i) stage-specific molecular events, (ii) most frequently observed genetic and epigenetic interdependencies in colon adenoma, and (iii) paths connecting key genes reported in CRC and associated events. The EpiGeNet framework offers improved capability for management and visualization of data on molecular events specific to CRC initiation and progression.
authors.affiliation: 1 European Institute for Systems Biology and Medicine (EISBM) , CIRI UMR CNRS 5308, CNRS-ENS-UCBL-INSERM, Université Claude Bernard, Lyon, France .
authors.forename: Irina
authors.initials: I
authors.lastname: Balaur
authors.affiliation: 1 European Institute for Systems Biology and Medicine (EISBM) , CIRI UMR CNRS 5308, CNRS-ENS-UCBL-INSERM, Université Claude Bernard, Lyon, France .
authors.forename: Mansoor
authors.initials: M
authors.lastname: Saqi
authors.affiliation: 2 Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland , Dublin, Ireland .
authors.forename: Ana
authors.initials: A
authors.lastname: Barat
authors.affiliation: 3 Rothamsted Research , Hertfordshire, United Kingdom .
authors.forename: Artem
authors.initials: A
authors.lastname: Lysenko
authors.affiliation: 1 European Institute for Systems Biology and Medicine (EISBM) , CIRI UMR CNRS 5308, CNRS-ENS-UCBL-INSERM, Université Claude Bernard, Lyon, France .
authors.forename: Alexander
authors.initials: A
authors.lastname: Mazein
authors.affiliation: 3 Rothamsted Research , Hertfordshire, United Kingdom .
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Rawlings
authors.affiliation: 4 Centre for Scientific Computing and Complex Systems Modelling, School of Computing, Dublin City University , Dublin, Ireland .
authors.forename: Heather J
authors.initials: HJ
authors.lastname: Ruskin
authors.affiliation: 1 European Institute for Systems Biology and Medicine (EISBM) , CIRI UMR CNRS 5308, CNRS-ENS-UCBL-INSERM, Université Claude Bernard, Lyon, France .
authors.forename: Charles
authors.initials: C
authors.lastname: Auffray
mesh_terms: D015179:Colorectal Neoplasms / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D016208:Databases, Factual; D044127:Epigenesis, Genetic; D053263:Gene Regulatory Networks; D006801:Humans; D012984:Software
keywords: colorectal cancer; computational molecular biology; epigenetics; graph database; molecular interdependencies; networks