Literature DB >> 14681442

SGMD: the Soybean Genomics and Microarray Database.

Nadim W Alkharouf1, Benjamin F Matthews.   

Abstract

The Soybean Genomics and Microarray Database (SGMD) attempts to provide an integrated view of the interaction of soybean with the soybean cyst nematode and contains genomic, EST and microarray data with embedded analytical tools allowing correlation of soybean ESTs with their gene expression profiles. SGMD provides analytical tools to mine the microarray data quickly by integrating many analysis methods within the database itself. The expression profiles of genes at time intervals during the first 8 days of nematode invasion is searchable by gene name or GenBank accession number. Recent developments include the addition of a searchable database for soybean cyst nematode ESTs and photographs of the invasion process at time points examined using microarrays. SGMD is completely accessible from the web at: http://psi081.ba.ars.usda.gov/SGMD/default.htm.

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Year:  2004        PMID： 14681442      PMCID： PMC308860          DOI： 10.1093/nar/gkh126

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  10 in total

1.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

Review 2.  Microarray databases: standards and ontologies.

Authors:  Christian J Stoeckert; Helen C Causton; Catherine A Ball
Journal:  Nat Genet       Date:  2002-12       Impact factor: 38.330

Review 3.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

4.  Functional and comparative bioinformatic analysis of expressed genes from wheat spikes infected with Fusarium graminearum.

Authors:  Warren M Kruger; Clara Pritsch; Shiaoman Chao; Gary J Muehlbauer
Journal:  Mol Plant Microbe Interact       Date:  2002-05       Impact factor: 4.171

5.  Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression.

Authors:  R M Ewing; A Ben Kahla; O Poirot; F Lopez; S Audic; J M Claverie
Journal:  Genome Res       Date:  1999-10       Impact factor: 9.043

6.  Profiling local gene expression changes associated with Eimeria maxima and Eimeria acervulina using cDNA microarray.

Authors:  W Min; H S Lillehoj; S Kim; J J Zhu; H Beard; N Alkharouf; B F Matthews
Journal:  Appl Microbiol Biotechnol       Date:  2003-04-24       Impact factor: 4.813

7.  Analysis of genes expressed during rice-Magnaporthe grisea interactions.

Authors:  S Kim; I P Ahn; Y H Lee
Journal:  Mol Plant Microbe Interact       Date:  2001-11       Impact factor: 4.171

8.  Ascaris suum: cDNA microarray analysis of 4th stage larvae (L4) during self-cure from the intestine.

Authors:  Motoko Morimoto; Dante Zarlenga; Hunter Beard; Nadim Alkharouf; Benjamin F Matthews; Joseph F Urban
Journal:  Exp Parasitol       Date:  2003 Jul-Aug       Impact factor: 2.011

9.  Analysis of expressed sequence tags from roots of resistant soybean infected by the soybean cyst nematode.

Authors:  Nadim Alkharouf; Rana Khan; Benjamin Matthews
Journal:  Genome       Date:  2004-04       Impact factor: 2.166

10.  Design and implementation of microarray gene expression markup language (MAGE-ML).

Authors:  Paul T Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce J Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Journal:  Genome Biol       Date:  2002-08-23       Impact factor: 13.583
  10 in total
  22 in total

1.  Mapping cell fate decisions that occur during soybean defense responses.

Authors:  Prachi D Matsye; Ranjit Kumar; Parsa Hosseini; Christina M Jones; Arianne Tremblay; Nadim W Alkharouf; Benjamin F Matthews; Vincent P Klink
Journal:  Plant Mol Biol       Date:  2011-10-11       Impact factor: 4.076

Review 2.  Emerging approaches to broaden resistance of soybean to soybean cyst nematode as supported by gene expression studies.

Authors:  Vincent P Klink; Benjamin F Matthews
Journal:  Plant Physiol       Date:  2009-08-12       Impact factor: 8.340

3.  Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode).

Authors:  Nadim W Alkharouf; Vincent P Klink; Imed B Chouikha; Hunter S Beard; Margaret H MacDonald; Susan Meyer; Halina T Knap; Rana Khan; Benjamin F Matthews
Journal:  Planta       Date:  2006-03-31       Impact factor: 4.116

4.  Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines).

Authors:  Vincent P Klink; Christopher C Overall; Nadim W Alkharouf; Margaret H Macdonald; Benjamin F Matthews
Journal:  J Biomed Biotechnol       Date:  2010-05-19

5.  A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode).

Authors:  Vincent P Klink; Parsa Hosseini; Prachi Matsye; Nadim W Alkharouf; Benjamin F Matthews
Journal:  Plant Mol Biol       Date:  2009-09-29       Impact factor: 4.076

6.  Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines).

Authors:  Vincent P Klink; Christopher C Overall; Nadim W Alkharouf; Margaret H MacDonald; Benjamin F Matthews
Journal:  Planta       Date:  2007-08-01       Impact factor: 4.116

7.  A correlation between host-mediated expression of parasite genes as tandem inverted repeats and abrogation of development of female Heterodera glycines cyst formation during infection of Glycine max.

Authors:  Vincent P Klink; Kyung-Hwan Kim; Veronica Martins; Margaret H Macdonald; Hunter S Beard; Nadim W Alkharouf; Seong-Kon Lee; Soo-Chul Park; Benjamin F Matthews
Journal:  Planta       Date:  2009-04-04       Impact factor: 4.116

8.  A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection.

Authors:  Vincent P Klink; Christopher C Overall; Nadim W Alkharouf; Margaret H MacDonald; Benjamin F Matthews
Journal:  Planta       Date:  2007-07-25       Impact factor: 4.116

9.  Protease inhibitor expression in soybean roots exhibiting susceptible and resistant interactions with soybean cyst nematode.

Authors:  Nahed A Rashed; Margaret H Macdonald; Benjamin F Matthews
Journal:  J Nematol       Date:  2008-06       Impact factor: 1.402

10.  Developing a systems biology approach to study disease progression caused by Heterodera glycines in Glycine max.

Authors:  Vincent P Klink; Christopher C Overall; Benjamin F Matthews
Journal:  Gene Regul Syst Bio       Date:  2007-06-05
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