Literature DB >> 19279703

Developmental biology and databases: how to archive, find and query gene expression patterns using the world wide web.

Chris Armit.   

Abstract

Systems biology has undergone an explosive growth in recent times. The staggering amount of expression data that can now be obtained from microarray chip analysis and high-throughput in situ screens has lent itself to the creation of large, terabyte-capacity databases in which to house gene expression patterns. Furthermore, innovative methods can be used to interrogate these databases and to link genomic information to functional information of embryonic cells, tissues and organs. These formidable advancements have led to the development of a whole host of online resources that have allowed biologists to probe the mysteries of growth and form with renewed zeal. This review seeks to highlight general features of these databases, and to identify the methods by which expression data can be retrieved.

Keywords:  cDNA micro-array; embryo; in situ hybridisation; ontology

Year:  2007        PMID: 19279703      PMCID: PMC2649618          DOI: 10.4161/org.3.2.4942

Source DB:  PubMed          Journal:  Organogenesis        ISSN: 1547-6278            Impact factor:   2.500


  7 in total

1.  A friendly statistics package for microarray analysis.

Authors:  P Sykacek; R A Furlong; G Micklem
Journal:  Bioinformatics       Date:  2005-09-27       Impact factor: 6.937

2.  Fates of the blastomeres of the 16-cell stage Xenopus embryo.

Authors:  S A Moody
Journal:  Dev Biol       Date:  1987-02       Impact factor: 3.582

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Authors:  J E Sulston; E Schierenberg; J G White; J N Thomson
Journal:  Dev Biol       Date:  1983-11       Impact factor: 3.582

4.  Fates of the blastomeres of the 32-cell-stage Xenopus embryo.

Authors:  S A Moody
Journal:  Dev Biol       Date:  1987-08       Impact factor: 3.582

5.  The cleavage stage origin of Spemann's Organizer: analysis of the movements of blastomere clones before and during gastrulation in Xenopus.

Authors:  D V Bauer; S Huang; S A Moody
Journal:  Development       Date:  1994-05       Impact factor: 6.868

6.  Evaluation of clustering algorithms for gene expression data.

Authors:  Susmita Datta; Somnath Datta
Journal:  BMC Bioinformatics       Date:  2006-12-12       Impact factor: 3.169

7.  Mouse Phenome Database (MPD).

Authors:  Molly A Bogue; Stephen C Grubb; Terry P Maddatu; Carol J Bult
Journal:  Nucleic Acids Res       Date:  2006-12-06       Impact factor: 16.971

  7 in total
  2 in total

Review 1.  Application of a systems approach to study developmental gene regulation.

Authors:  Joshua W K Ho
Journal:  Biophys Rev       Date:  2012-09-01

2.  Stage-specific signaling pathways during murine testis development and spermatogenesis: A pathway-based analysis to quantify developmental dynamics.

Authors:  Susanna H Wegner; Xiaozhong Yu; Sara Pacheco Shubin; William C Griffith; Elaine M Faustman
Journal:  Reprod Toxicol       Date:  2014-11-25       Impact factor: 3.143

  2 in total

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