Flyexpress: Visual mining of spatiotemporal patterns for genes and publications in drosophila embryogenesis

Sudhir Kumar, Charlotte Konikoff, Bernard Van emden, Christopher Busick, Kailah T. Davis, Shuiwang Ji, Lin Wei Wu, Hector Ramos, Thomas Brody, Sethuraman Panchanathan, Jieping Ye, Timothy L. Karr, Kristyn Gerold, Michael Mccutchan, Stuart Newfeld

Research output: Contribution to journalArticle

38 Scopus citations

Abstract

Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects. We have developed a unique knowledge base (FlyExpress) to facilitate visual mining of images from Drosophila melanogaster embryogenesis. By clicking on specific locations in pictures of fly embryos from different stages of development and different visual projections, users can produce a list of genes and publications instantly. In FlyExpress, each queryable embryo picture is a heat-map that captures the expression patterns of more than 4500 genes and more than 2600 published articles. In addition, one can view spatial patterns for particular genes over time as well as find other genes with similar expression patterns at a given developmental stage. Therefore, FlyExpress is a unique tool for mining spatiotemporal expression patterns in a format readily accessible to the scientific community.

Original languageEnglish (US)
Article numberbtr567
Pages (from-to)3319-3320
Number of pages2
JournalBioinformatics
Volume27
Issue number23
DOIs
StatePublished - Dec 1 2011

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint Dive into the research topics of 'Flyexpress: Visual mining of spatiotemporal patterns for genes and publications in drosophila embryogenesis'. Together they form a unique fingerprint.

  • Cite this

    Kumar, S., Konikoff, C., Van emden, B., Busick, C., Davis, K. T., Ji, S., Wu, L. W., Ramos, H., Brody, T., Panchanathan, S., Ye, J., Karr, T. L., Gerold, K., Mccutchan, M., & Newfeld, S. (2011). Flyexpress: Visual mining of spatiotemporal patterns for genes and publications in drosophila embryogenesis. Bioinformatics, 27(23), 3319-3320. [btr567]. https://doi.org/10.1093/bioinformatics/btr567