Sub-Challenge 3: Inter-Species Pathway Perturbation Prediction

Sub-Challenge 3: Inter-Species Pathway Perturbation Prediction

Sub-Challenge 3 is closed

 

Description

Sub-challenge 3 requires the prediction of gene sets representing pathways/biological processes in Subset B of human cells. Participants, based on the corresponding data in rat, are asked to order the gene sets from the most to the least active, for each stimulus,. This ordering should be based on the enrichment of differentially expressed genes in the gene set with respect to control conditions. 

Figure SC3.A: Sub-challenge 3 requires the prediction of gene sets that are the most to least enriched among differentially expressed genes, with respect to control for each stimulus in Subset B in human based on the corresponding data in rat. The gene sets are provided and were chosen to allow the assessment of a range of functional processes and pathways in the cell.  

Background

The biomedical field has generally worked under the assumption that biological processes in mice or rats will correspond to biological processes in humans under analogous conditions. However, comparisons of transcriptomic data have pointed to the difficulties of performing a translation based uniquely on the expression level of orthologous genes. The difficulty could lie at several levels. For example, orthologous genes may have diverged in function and play different roles in the cell. One potential method to improve translation is to take a pathway-centric view and consider whether similar pathways in rat and human are activated under analogous conditions.

 

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