Hepatotoxicity associated gene lists

Under diXa Milestones 8.2, 8.3, and 8.5 hepatotoxicity-associated gene lists were developed from text mining databases such as CTD, LoMA, Gataca, and MalaCards and from human liver omics data present in ArrayExpress. These gene lists were tested for their relevance in a pathway analysis and an evaluation of the best performing gene lists was presented in a recent paper, which can be found HERE . The methods and results are also described in Milestone report 8.8, available HERE.

Relevant gene lists identified in this pathway analysis represent interesting candidates to convert to SBML format which is a representation format, based on XML, for communicating and storing computational models of biological processes and offers a higher degree of complexity than for example GPML. For this conversion a CytoScape plugin called BiNoM (version 2.5) was identified which enables easy transformation from TXT or GPML to SBML format. However, this will require the use of a network-building tool, such as the one offered by ConsensusPathDB, as explained in Milestone report 8.8.

Researchers interested in these gene lists can download them for their own data analyses and edit or update these lists as needed.


Text mining database gene lists (GPML versions, TXT versions)

Human liver omics database gene lists (GPML versions, TXT versions)