CLIP-GENE: A web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments

Benjamin Hur, Sangsoo Lim, Heejoon Chae, Seokjun Seo, Sunwon Lee, Jaewoo Kang, Sun Kim

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Article number57
JournalBiology Direct
Volume11
Issue number1
DOIs
Publication statusPublished - 2016 Oct 24

Fingerprint

Transcription factors
Prioritization
prioritization
Transcription Factor
Web services
Web Services
Mouse
Transcription Factors
transcription factors
Genes
Gene
gene
mice
Experiment
genes
experiment
Experiments
Gene Knockout Techniques
gene targeting
Context

Keywords

  • Gene prioritization
  • Gene selection
  • Knockout mouse
  • Web tool

ASJC Scopus subject areas

  • Immunology
  • Ecology, Evolution, Behavior and Systematics
  • Modelling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

Cite this

CLIP-GENE : A web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments. / Hur, Benjamin; Lim, Sangsoo; Chae, Heejoon; Seo, Seokjun; Lee, Sunwon; Kang, Jaewoo; Kim, Sun.

In: Biology Direct, Vol. 11, No. 1, 57, 24.10.2016.

Research output: Contribution to journalArticle

Hur, Benjamin ; Lim, Sangsoo ; Chae, Heejoon ; Seo, Seokjun ; Lee, Sunwon ; Kang, Jaewoo ; Kim, Sun. / CLIP-GENE : A web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments. In: Biology Direct. 2016 ; Vol. 11, No. 1.
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