Literature DB >> 12424128

SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis.

Carlo Colantuoni1, George Henry, Scott Zeger, Jonathan Pevsner.   

Abstract

SNOMAD is a collection of algorithms for the normalization and standardization of gene expression datasets derived from diverse biological and technological sources. In addition to conventional transformations and visualization tools, SNOMAD includes two non-linear transformations which correct for bias and variance which are non-uniformly distributed across the range of microarray element signal intensities: (1). Local mean normalization; and (2). Local variance correction (Z-score generation using a locally calculated standard deviation).

Mesh:

Year:  2002        PMID: 12424128     DOI: 10.1093/bioinformatics/18.11.1540

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  46 in total

1.  Identification and handling of artifactual gene expression profiles emerging in microarray hybridization experiments.

Authors:  Leonid Brodsky; Andrei Leontovich; Michael Shtutman; Elena Feinstein
Journal:  Nucleic Acids Res       Date:  2004-03-03       Impact factor: 16.971

2.  Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis.

Authors:  Pingli Lu; Xinwei Han; Ji Qi; Jiange Yang; Asela J Wijeratne; Tao Li; Hong Ma
Journal:  Genome Res       Date:  2011-11-21       Impact factor: 9.043

Review 3.  DNA microarrays--techniques and applications in microbial systems.

Authors:  T Majtán; G Bukovská; J Timko
Journal:  Folia Microbiol (Praha)       Date:  2004       Impact factor: 2.099

4.  Defining the sequence-recognition profile of DNA-binding molecules.

Authors:  Christopher L Warren; Natasha C S Kratochvil; Karl E Hauschild; Shane Foister; Mary L Brezinski; Peter B Dervan; George N Phillips; Aseem Z Ansari
Journal:  Proc Natl Acad Sci U S A       Date:  2006-01-17       Impact factor: 11.205

5.  Goulphar: rapid access and expertise for standard two-color microarray normalization methods.

Authors:  Sophie Lemoine; Florence Combes; Nicolas Servant; Stéphane Le Crom
Journal:  BMC Bioinformatics       Date:  2006-10-23       Impact factor: 3.169

6.  CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.

Authors:  Weil Lai; Vidhu Choudhary; Peter J Park
Journal:  Bioinformatics       Date:  2008-02-22       Impact factor: 6.937

7.  Sex of the cell dictates its response: differential gene expression and sensitivity to cell death inducing stress in male and female cells.

Authors:  Carlos Penaloza; Brian Estevez; Shari Orlanski; Marianna Sikorska; Roy Walker; Catherine Smith; Brandon Smith; Richard A Lockshin; Zahra Zakeri
Journal:  FASEB J       Date:  2009-02-03       Impact factor: 5.191

8.  The temporal program of chromosome replication: genomewide replication in clb5{Delta} Saccharomyces cerevisiae.

Authors:  Heather J McCune; Laura S Danielson; Gina M Alvino; David Collingwood; Jeffrey J Delrow; Walton L Fangman; Bonita J Brewer; M K Raghuraman
Journal:  Genetics       Date:  2008-10-01       Impact factor: 4.562

9.  Application of functional genomics to pathway optimization for increased isoprenoid production.

Authors:  Lance Kizer; Douglas J Pitera; Brian F Pfleger; Jay D Keasling
Journal:  Appl Environ Microbiol       Date:  2008-03-14       Impact factor: 4.792

10.  Slow proliferation as a biological feature of colorectal cancer metastasis.

Authors:  A Anjomshoaa; S Nasri; B Humar; J L McCall; A Chatterjee; H-S Yoon; L McNoe; M A Black; A E Reeve
Journal:  Br J Cancer       Date:  2009-08-04       Impact factor: 7.640

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