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

35 Citations (Scopus)

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 2011

Fingerprint

Embryogenesis
Spatio-temporal Patterns
Drosophilidae
Drosophila
Embryonic Development
Publications
Mining
Genes
Gene
Embryo
Embryonic Structures
Image Annotation
Data Mining
Knowledge Bases
Spatial Pattern
Drosophila melanogaster
Research
Diptera
Knowledge Base
Vision

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Flyexpress : Visual mining of spatiotemporal patterns for genes and publications in drosophila embryogenesis. / Kumar, Sudhir; Konikoff, Charlotte; Van emden, Bernard; Busick, Christopher; Davis, Kailah T.; Ji, Shuiwang; Wu, Lin Wei; Ramos, Hector; Brody, Thomas; Panchanathan, Sethuraman; Ye, Jieping; Karr, Timothy L.; Gerold, Kristyn; Mccutchan, Michael; Newfeld, Stuart.

In: Bioinformatics, Vol. 27, No. 23, btr567, 12.2011, p. 3319-3320.

Research output: Contribution to journalArticle

Kumar, S, Konikoff, C, Van emden, B, Busick, C, Davis, KT, Ji, S, Wu, LW, Ramos, H, Brody, T, Panchanathan, S, Ye, J, Karr, TL, Gerold, K, Mccutchan, M & Newfeld, S 2011, 'Flyexpress: Visual mining of spatiotemporal patterns for genes and publications in drosophila embryogenesis', Bioinformatics, vol. 27, no. 23, btr567, pp. 3319-3320. https://doi.org/10.1093/bioinformatics/btr567
Kumar, Sudhir ; Konikoff, Charlotte ; Van emden, Bernard ; Busick, Christopher ; Davis, Kailah T. ; Ji, Shuiwang ; Wu, Lin Wei ; Ramos, Hector ; Brody, Thomas ; Panchanathan, Sethuraman ; Ye, Jieping ; Karr, Timothy L. ; Gerold, Kristyn ; Mccutchan, Michael ; Newfeld, Stuart. / Flyexpress : Visual mining of spatiotemporal patterns for genes and publications in drosophila embryogenesis. In: Bioinformatics. 2011 ; Vol. 27, No. 23. pp. 3319-3320.
@article{8302193f871d4f2c896477c16c148e09,
title = "Flyexpress: Visual mining of spatiotemporal patterns for genes and publications in drosophila embryogenesis",
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.",
author = "Sudhir Kumar and Charlotte Konikoff and {Van emden}, Bernard and Christopher Busick and Davis, {Kailah T.} and Shuiwang Ji and Wu, {Lin Wei} and Hector Ramos and Thomas Brody and Sethuraman Panchanathan and Jieping Ye and Karr, {Timothy L.} and Kristyn Gerold and Michael Mccutchan and Stuart Newfeld",
year = "2011",
month = "12",
doi = "10.1093/bioinformatics/btr567",
language = "English (US)",
volume = "27",
pages = "3319--3320",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "23",

}

TY - JOUR

T1 - Flyexpress

T2 - Visual mining of spatiotemporal patterns for genes and publications in drosophila embryogenesis

AU - Kumar, Sudhir

AU - Konikoff, Charlotte

AU - Van emden, Bernard

AU - Busick, Christopher

AU - Davis, Kailah T.

AU - Ji, Shuiwang

AU - Wu, Lin Wei

AU - Ramos, Hector

AU - Brody, Thomas

AU - Panchanathan, Sethuraman

AU - Ye, Jieping

AU - Karr, Timothy L.

AU - Gerold, Kristyn

AU - Mccutchan, Michael

AU - Newfeld, Stuart

PY - 2011/12

Y1 - 2011/12

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=82255181421&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=82255181421&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btr567

DO - 10.1093/bioinformatics/btr567

M3 - Article

C2 - 21994220

AN - SCOPUS:82255181421

VL - 27

SP - 3319

EP - 3320

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 23

M1 - btr567

ER -