Document Detail


Novel algorithm for transcriptome analysis.
MedLine Citation:
PMID:  17003079     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A growing body of evidence implicates the oocyte as a key regulator of ovarian folliculogenesis and early embryonic development. We have screened bovine cDNA microarrays (containing expressed sequence tags representing >15,000 unique genes) with Cy3- and Cy5-labeled cDNA derived from bovine oocyte samples collected at two different stages of meiotic maturation (germinal vesicle vs. metaphase II; n = 3 samples per group). Here, we present a novel data analysis approach that uses all available information from above experiments to obtain and index the transcriptome of bovine oocytes and changes in transcriptome composition in response to meiotic maturation. Signal intensities (Fg) for all housekeeping genes were omitted prior to analysis. A local threshold for gene expression was computed as background intensity (Bg) plus 2 times the standard deviation of background and foreground signals. Within each array, data were normalized by the LOWESS procedure. Subsequently, a two-stage mixed model was fitted to remove systematic variations. In the first stage, the response was the LOWESS normalized Fg with treatment as a fixed effect. In stage 2, the residuals from stage 1 were analyzed in a gene-specific model that included treatment group and spots nested within patch and array. A test for the difference between least squares means for the treatment effect was performed. A false discovery rate (FDR) adjustment on the p values for the difference was carried out. This novel algorithm was compared with approaches that ignore the FDR and the threshold described herein and stark differences obtained.
Authors:
Peter M Saama; Osman V Patel; Anilkumar Bettegowda; James J Ireland; George W Smith
Related Documents :
15867429 - Multi-species microarrays reveal the effect of sequence divergence on gene expression p...
16305329 - Evaluation of experimental designs for two-color cdna microarrays.
21396889 - Identification and characterization of another 4-nitrophenol degradation gene cluster, ...
21184059 - Bioconversion of substituted naphthalenes and β-eudesmol with the cytochrome p450 bm3 ...
17106189 - Changes in gene expression pattern following granulocyte colony-stimulating factor admi...
16098629 - Multievidence microarray mining.
10630419 - Identification of phenobarbitone-modulated genes in mouse liver by differential display.
10713069 - Two distinct nucleosome alterations characterize chromatin remodeling at the saccharomy...
12428539 - Genetics of asthma.
Publication Detail:
Type:  Comparative Study; Evaluation Studies; Journal Article; Research Support, Non-U.S. Gov't     Date:  2006-09-26
Journal Detail:
Title:  Physiological genomics     Volume:  28     ISSN:  1531-2267     ISO Abbreviation:  Physiol. Genomics     Publication Date:  2006 Dec 
Date Detail:
Created Date:  2006-12-14     Completed Date:  2007-02-22     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9815683     Medline TA:  Physiol Genomics     Country:  United States    
Other Details:
Languages:  eng     Pagination:  62-6     Citation Subset:  IM    
Affiliation:
Genus Plc., Hendersonville, Tennessee, USA.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Algorithms*
Animals
Cattle
Female
Gene Expression Profiling*
Oligonucleotide Array Sequence Analysis / methods
Oocytes / metabolism
Pregnancy
RNA / metabolism
Transcription, Genetic*
Chemical
Reg. No./Substance:
63231-63-0/RNA

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  Dissociation of stimulus relevance and saliency factors during shifts of visuospatial attention.
Next Document:  Relief of acute pain in chronic idiopathic gastroparesis with intravenous phentolamine.