Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data

doi:10.1186/gb-2008-9-1-r23

Genome Biology

Volume 9
Issue 1

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Lee CK
Sunkin SM
Kuan C
Thompson CL
Pathak S
Ng L
Lau C
Fischer S
Mortrud M
Slaughterbeck C
Jones A
Lein E
Hawrylycz M

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Lee CK
Sunkin SM
Kuan C
Thompson CL
Pathak S
Ng L
Lau C
Fischer S
Mortrud M
Slaughterbeck C
Jones A
Lein E
Hawrylycz M
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Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data

Chang-Kyu Lee , Susan M Sunkin , Chihchau Kuan , Carol L Thompson , Sayan Pathak , Lydia Ng , Chris Lau , Shanna Fischer , Marty Mortrud , Cliff Slaughterbeck , Allan Jones , Ed Lein and Michael Hawrylycz

Allen Institute for Brain Science, N. 34th Street, Seattle, WA 98103, USA

author email corresponding author email

Genome Biology 2008, 9:R23doi:10.1186/gb-2008-9-1-r23


Published:	30 January 2008

Subject areas: Bioinformatics, Methods, Neurobiology

Abstract

With the emergence of genome-wide colorimetric in situ hybridization (ISH) data sets such as the Allen Brain Atlas, it is important to understand the relationship between this gene expression modality and those derived from more quantitative based technologies. This study introduces a novel method for standardized relative quantification of colorimetric ISH signal that enables a large-scale cross-platform expression level comparison of ISH with two publicly available microarray brain data sources.