Literature DB >> 16968907

A discussion of statistical methods for design and analysis of microarray experiments for plant scientists.

Dan Nettleton1.   

Abstract

Mesh：

Year:  2006        PMID： 16968907      PMCID： PMC1560901          DOI： 10.1105/tpc.106.041616

Source DB:  PubMed          Journal:  Plant Cell        ISSN： 1040-4651            Impact factor:   11.277


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  27 in total

1.  Assessing gene significance from cDNA microarray expression data via mixed models.

Authors:  R D Wolfinger; G Gibson; E D Wolfinger; L Bennett; H Hamadeh; P Bushel; C Afshari; R S Paules
Journal:  J Comput Biol       Date:  2001       Impact factor: 1.479

Review 2.  Statistical design and the analysis of gene expression microarray data.

Authors:  M K Kerr; G A Churchill
Journal:  Genet Res       Date:  2001-04       Impact factor: 1.588

3.  Analysis of variance for gene expression microarray data.

Authors:  M K Kerr; M Martin; G A Churchill
Journal:  J Comput Biol       Date:  2000       Impact factor: 1.479

4.  Statistical design of reverse dye microarrays.

Authors:  K Dobbin; J H Shih; R Simon
Journal:  Bioinformatics       Date:  2003-05-01       Impact factor: 6.937

5.  Factorial and time course designs for cDNA microarray experiments.

Authors:  G F V Glonek; P J Solomon
Journal:  Biostatistics       Date:  2004-01       Impact factor: 5.899

Review 6.  Design issues for cDNA microarray experiments.

Authors:  Yee Hwa Yang; Terry Speed
Journal:  Nat Rev Genet       Date:  2002-08       Impact factor: 53.242

7.  Quantitative trait loci associated with adventitious shoot formation in tissue culture and the program of shoot development in Arabidopsis.

Authors:  Sonia Lall; Dan Nettleton; Rhonda DeCook; Ping Che; Stephen H Howell
Journal:  Genetics       Date:  2004-08       Impact factor: 4.562

Review 8.  Microarray data analysis: from disarray to consolidation and consensus.

Authors:  David B Allison; Xiangqin Cui; Grier P Page; Mahyar Sabripour
Journal:  Nat Rev Genet       Date:  2006-01       Impact factor: 53.242

9.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

10.  A random variance model for detection of differential gene expression in small microarray experiments.

Authors:  George W Wright; Richard M Simon
Journal:  Bioinformatics       Date:  2003-12-12       Impact factor: 6.937
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  30 in total

1.  Role of OsNPR1 in rice defense program as revealed by genome-wide expression analysis.

Authors:  Shoji Sugano; Chang-Jie Jiang; Shin-Ichi Miyazawa; Chisato Masumoto; Katsumi Yazawa; Nagao Hayashi; Masaki Shimono; Akira Nakayama; Mitsue Miyao; Hiroshi Takatsuji
Journal:  Plant Mol Biol       Date:  2010-10-07       Impact factor: 4.076

2.  Quantitative proteomics in plants: choices in abundance.

Authors:  Jay J Thelen; Scott C Peck
Journal:  Plant Cell       Date:  2007-11-30       Impact factor: 11.277

3.  Establishing a framework for the Ad/abaxial regulatory network of Arabidopsis: ascertaining targets of class III homeodomain leucine zipper and KANADI regulation.

Authors:  Brenda J Reinhart; Tie Liu; Nicole R Newell; Enrico Magnani; Tengbo Huang; Randall Kerstetter; Scott Michaels; M Kathryn Barton
Journal:  Plant Cell       Date:  2013-09-27       Impact factor: 11.277

4.  Finding differentially expressed genes in two-channel DNA microarray datasets: how to increase reliability of data preprocessing.

Authors:  Ana Rotter; Matjaz Hren; Spela Baebler; Andrej Blejec; Kristina Gruden
Journal:  OMICS       Date:  2008-09

5.  Transcriptional profiling of Zea mays roots reveals roles for jasmonic acid and terpenoids in resistance against Phytophthora cinnamomi.

Authors:  Jane Alisa Allardyce; James Edward Rookes; Hashmath Inayath Hussain; David Miles Cahill
Journal:  Funct Integr Genomics       Date:  2013-02-22       Impact factor: 3.410

6.  Resistance to Botrytis cinerea in sitiens, an abscisic acid-deficient tomato mutant, involves timely production of hydrogen peroxide and cell wall modifications in the epidermis.

Authors:  Bob Asselbergh; Katrien Curvers; Soraya C Franca; Kris Audenaert; Marnik Vuylsteke; Frank Van Breusegem; Monica Höfte
Journal:  Plant Physiol       Date:  2007-06-15       Impact factor: 8.340

7.  Functional definition of outer membrane proteins involved in preprotein import into mitochondria.

Authors:  Ryan Lister; Chris Carrie; Owen Duncan; Lois H M Ho; Katharine A Howell; Monika W Murcha; James Whelan
Journal:  Plant Cell       Date:  2007-11-02       Impact factor: 11.277

8.  Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis.

Authors:  Lois H M Ho; Estelle Giraud; Vindya Uggalla; Ryan Lister; Rachel Clifton; Angela Glen; Dave Thirkettle-Watts; Olivier Van Aken; James Whelan
Journal:  Plant Physiol       Date:  2008-06-20       Impact factor: 8.340

9.  Drought response in the spikes of barley: gene expression in the lemma, palea, awn, and seed.

Authors:  Tilahun Abebe; Kalpalatha Melmaiee; Virginia Berg; Roger P Wise
Journal:  Funct Integr Genomics       Date:  2009-11-20       Impact factor: 3.410

10.  Complex I dysfunction redirects cellular and mitochondrial metabolism in Arabidopsis.

Authors:  Marie Garmier; Adam J Carroll; Etienne Delannoy; Corinne Vallet; David A Day; Ian D Small; A Harvey Millar
Journal:  Plant Physiol       Date:  2008-09-10       Impact factor: 8.340
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