A Quantitative Overview to Gene Expression Profiling in Animal Genetics

1
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
GP3xCLI
GenePix Post-Processing By CSIRO Livestock
Industries
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
2
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
GP3xCLI
Introduction

• Each microarray hybridisation generates a large
  amount of data resulting from the scanning of two
  images (one red, one green).
• It is both tedious and prone to human error to
  visually assess the quality of each spot on the
  microarray.
• GP3xCLI is an automated AWK-based script to
  assess the quality of raw microarray data
  captured using the GenePix optical scanner.
• Executed from the prompt line, GP3xCLI
  incorporates tools such as
• A2PS ? ASCII to Postscript translator
• GNUPLOT ? interactive plotting utility
• PS2PDF ? public domain postscript to PDF
  converter
• On execution, GP3xCLI generates a 2-page PDF
  file.
• Inspired by GP3 (http//www.bch.msu.edu/zacharet/
  microarray/GP3.html), GP3xCLI is not intended to
  perform any real analysis (eg. Correction,
  filtering, normalisation).
• Quality assessment is based on standard
• Summary Statistics
• Diagnostic plots

Armidale Animal Breeding Summer Course, UNE, Feb.
2006
3
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
GP3xCLI
Summary Statistics

• Total Number of Spots.
• Number of Spots by Quality Flag (generated by the
  scanner).
• For each channel (Red and Green), Number of Spots
  for which the foreground is less than the
  background intensity signal.
• Optimality of Log-transformation ? Amount of data
  left by each threshold of Mean to Median
  correlation.
• Number of Repetitions by Genes
• N, Mean, Std, Min and Max for Log-Ratio
  (Red/Green) and average (RedGreen) intensities

Armidale Animal Breeding Summer Course, UNE, Feb.
2006
4
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
GP3xCLI
Summary Statistics
Valid Spots - Foreground gt Backgrond -
Quality Flag 0
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
5
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
GP3xCLI
Diagnostic Plots
NB Only for Valid Spot - Foreground gt
Backgrond - Quality Flag 0
RED versus GREEN
Scatters
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
6
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
GP3xCLI
Diagnostic Plots
NB Only for Valid Spot - Foreground gt
Backgrond - Quality Flag 0
RED and GREEN
Densities
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
7
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
GP3xCLI
Diagnostic Plots
NB Only for Valid Spot - Foreground gt
Backgrond - Quality Flag 0
RED to GREEN
Ratios
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
8
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
GP3xCLI
Application
The Diets Experiment 3 Diets,10 Animals,14
Microarrays
Available at http//www.livestockgenomics.csiro.a
u/downloads/Keren/
Armidale Animal Breeding Summer Course, UNE, Feb.
2006