Sub-Challenge 2: Inter-Species Protein Phosphorylation Prediction

Sub-Challenge 2: Inter-Species Protein Phosphorylation Prediction

Sub-Challenge 2 is closed

 

Description

Sub-challenge 2 requires the prediction of the activation status of human phosphoprotein based on equivalent data from homologous phosphoproteins in rat. The participants can use the activation status of rat phosphoprotein in Subset B to predict the activation status of human phosphoprotein in Subset B (Fig. SC2.A). The dataset includes the phosphorylation status of 16 different proteins covering diverse pathways. Predictions can be based on translation from rat phosphoprotein to human phosphoprotein directly. Alternatively, participants can use the data in Subset A to develop a mapping from GEx data to P data in human as training. After appropriate mapping of orthologs, the developed mapping from GEx to P in human can then be applied to rat GEx data in Subset B as a method to predict the human P data in Subset B.   

Figure SC2.A: Sub-challenge 2 requires the prediction of the activation status of human phosphoprotein based on analogous phosphoproteins data in rat. Rat phosphoprotein data in Subset B, collected with 26 different stimuli, is provided for training. 

Background

For more than a decade, transcriptomics microarray gene expression profiles have been widely used in research to investigate genome-wide perturbations of the biological systems under various conditions (e.g. chemical, disease, environmental, mutation, etc.). However, the observed gene expression regulation is already the result of a cascade of upstream signaling events going from the cell membrane to the nucleus. Therefore, acquiring phosphoproteomic data can additionally provide a more comprehensive view of cellular dynamics. In terms of comparability/translatability between species, the field has acknowledged that there can be difficulties in discerning clear relationships between the genes of two species, sometimes even for genes that appear to be orthologous. Although very similar in sequence, genes may diverge in function or take on new roles. Such features can limit simple translation of the functional roles of similar genes from one species to another. Therefore this challenge is posed at the protein level to assess the translatability of phosphorylation status of different proteins that cover a range of diverse cellular processes.

 

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