Motivation: Transcriptome data from the gene knockout experiment in mouse is widely used to investigate functions of genes and relationship to phenotypes. When a gene is knocked out, it is important to identify which genes are affected by the knockout gene. Existing methods, including differentially expressed gene (DEG) methods, can be used for the analysis. However, existing methods require cutoff values to select candidate genes, which can produce either too many false positives or false negatives. This hurdle can be addressed either by improving the accuracy of gene selection or by providing a method to rank candidate genes effectively, or both. Prioritization of candidate genes should consider the goals or context of the knockout experiment. As of now, there are no tools designed for both selecting and prioritizing genes from the mouse knockout data. Hence, the necessity of a new tool arises. Results: In this study, we present CLIP-GENE, a web service that selects gene markers by utilizing differentially expressed genes, mouse transcription factor (TF) network, and single nucleotide variant information. Then, protein-protein interaction network and literature information are utilized to find genes that are relevant to the phenotypic differences. One of the novel features is to allow researchers to specify their contexts or hypotheses in a set of keywords to rank genes according to the contexts that the user specify. We believe that CLIP-GENE will be useful in characterizing functions of TFs in mouse experiments. Availability: http://epigenomics.snu.ac.kr/CLIP-GENE Reviewers: This article was reviewed by Dr. Lee and Dr. Pongor.
Bibliographical noteFunding Information:
This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Ministry of Science, ICT & Future Planning (2012M3A9D1054622), Next-Generation Information Computing Development Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Science, ICT & Future Planning (No.NRF-2012M3C4A7033341), and Collaborative Genome Program for Fostering New Post-Genome industry through the National Research Foundation of Korea(NRF) funded by the Ministry of Science ICT and Future Planning (NRF-2014M3C9A3063541).
© 2016 The Author(s).
- Gene prioritization
- Gene selection
- Knockout mouse
- Web tool
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Modelling and Simulation
- General Biochemistry,Genetics and Molecular Biology
- General Agricultural and Biological Sciences
- Applied Mathematics