Literature DB >> 26519061

How to Use the Candida Genome Database.

Marek S Skrzypek1, Jonathan Binkley1, Gavin Sherlock2.   

Abstract

Studying Candida biology requires access to genomic sequence data in conjunction with experimental information that provides functional context to genes and proteins. The Candida Genome Database (CGD) integrates functional information about Candida genes and their products with a set of analysis tools that facilitate searching for sets of genes and exploring their biological roles. This chapter describes how the various types of information available at CGD can be searched, retrieved, and analyzed. Starting with the guided tour of the CGD Home page and Locus Summary page, this unit shows how to navigate the various assemblies of the C. albicans genome, how to use Gene Ontology tools to make sense of large-scale data, and how to access the microarray data archived at CGD.

Entities:  

Keywords:  Candida; Expression analysis; GO slim; Gene ontology; Genome database

Mesh：

Year:  2016        PMID： 26519061      PMCID： PMC4896156          DOI： 10.1007/978-1-4939-3052-4_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  13 in total

1.  GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.

Authors:  Elizabeth I Boyle; Shuai Weng; Jeremy Gollub; Heng Jin; David Botstein; J Michael Cherry; Gavin Sherlock
Journal:  Bioinformatics       Date:  2004-08-05       Impact factor: 6.937

2.  Textpresso: an ontology-based information retrieval and extraction system for biological literature.

Authors:  Hans-Michael Müller; Eimear E Kenny; Paul W Sternberg
Journal:  PLoS Biol       Date:  2004-09-21       Impact factor: 8.029

3.  Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser.

Authors:  David A Fitzpatrick; Peadar O'Gaora; Kevin P Byrne; Geraldine Butler
Journal:  BMC Genomics       Date:  2010-05-10       Impact factor: 3.969

4.  The diploid genome sequence of Candida albicans.

Authors:  Ted Jones; Nancy A Federspiel; Hiroji Chibana; Jan Dungan; Sue Kalman; B B Magee; George Newport; Yvonne R Thorstenson; Nina Agabian; P T Magee; Ronald W Davis; Stewart Scherer
Journal:  Proc Natl Acad Sci U S A       Date:  2004-05-03       Impact factor: 11.205

5.  Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure.

Authors:  Dale Muzzey; Katja Schwartz; Jonathan S Weissman; Gavin Sherlock
Journal:  Genome Biol       Date:  2013       Impact factor: 13.583

6.  Saccharomyces Genome Database provides mutant phenotype data.

Authors:  Stacia R Engel; Rama Balakrishnan; Gail Binkley; Karen R Christie; Maria C Costanzo; Selina S Dwight; Dianna G Fisk; Jodi E Hirschman; Benjamin C Hitz; Eurie L Hong; Cynthia J Krieger; Michael S Livstone; Stuart R Miyasato; Robert Nash; Rose Oughtred; Julie Park; Marek S Skrzypek; Shuai Weng; Edith D Wong; Kara Dolinski; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971

7.  InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Authors:  Gabriel Ostlund; Thomas Schmitt; Kristoffer Forslund; Tina Köstler; David N Messina; Sanjit Roopra; Oliver Frings; Erik L L Sonnhammer
Journal:  Nucleic Acids Res       Date:  2009-11-05       Impact factor: 16.971

8.  Comparative genome analysis and gene finding in Candida species using CGOB.

Authors:  Sarah L Maguire; Seán S ÓhÉigeartaigh; Kevin P Byrne; Markus S Schröder; Peadar O'Gaora; Kenneth H Wolfe; Geraldine Butler
Journal:  Mol Biol Evol       Date:  2013-03-13       Impact factor: 16.240

9.  Using GBrowse 2.0 to visualize and share next-generation sequence data.

Authors:  Lincoln D Stein
Journal:  Brief Bioinform       Date:  2013-02-01       Impact factor: 11.622

10.  Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes.

Authors:  Marco van het Hoog; Timothy J Rast; Mikhail Martchenko; Suzanne Grindle; Daniel Dignard; Hervé Hogues; Christine Cuomo; Matthew Berriman; Stewart Scherer; B B Magee; Malcolm Whiteway; Hiroji Chibana; André Nantel; P T Magee
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583
View more
  2 in total

1.  Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens.

Authors:  Reinhard Guthke; Silvia Gerber; Theresia Conrad; Sebastian Vlaic; Saliha Durmuş; Tunahan Çakır; F E Sevilgen; Ekaterina Shelest; Jörg Linde
Journal:  Front Microbiol       Date:  2016-04-22       Impact factor: 5.640

2.  Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling.

Authors:  Jana Maršíková; Derek Wilkinson; Otakar Hlaváček; Gregor D Gilfillan; Alexandru Mizeranschi; Timothy Hughes; Markéta Begany; Stanislava Rešetárová; Libuše Váchová; Zdena Palková
Journal:  BMC Genomics       Date:  2017-10-23       Impact factor: 3.969
  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.