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

Table 2 Gene selection for ISH and microarray expression comparison

	All genes	Genes with Entrez ID	One-to-one probe/gene mapping	Consistent present/absent call	Present and consistent
ISH (ABA)
Striatum	25,739	21,677	17,066	16,877	8,919
Cortex	25,749	21,683	17,077	16,848	11,358
Cerebellum	25,754	21,690	17,075	16,850	11,393
Hippocampus	25,766	21,691	17,074	16,897	11,465
Olfactory bulb	25,748	21,686	17,078	16,853	11,979
Hypothalamus	25,715	21,652	16,593	16,465	7,188
Microarray (Teragenomics)
Striatum	12,488	11,779	7,062	6,026	3,499
Cortex	12,488	11,779	7,062	5,958	3,488
Cerebellum	12,488	11,779	7,062	6,066	3,470
Hippocampus	12,488	11,779	7,062	5,997	3,363
Olfactory bulb	12,488	11,779	7,062	5,987	3,593
Hypothalamus	12,488	11,779	7,062	6,099	4,000
Microarray (GNF)
Striatum	31,770	26,982	13,582	11,713	3,438
Cortex	31,770	26,982	13,582	12,845	4,746
Cerebellum	31,770	26,982	13,582	11,773	4,121
Hippocampus	31,770	26,982	13,582	11,777	3,837
Olfactory bulb	31,770	26,982	13,582	11,885	4,123
Hypothalamus	31,770	26,982	13,582	11,869	4,341

Tabulated numbers show the number of genes satisfying the given criteria. Consistent present/absent reduces gene counts from one-to-one probe/gene mapping for genes with inconsistent replicates or genes with ambiguous expression call. (The ABA data contain a limited number of sagittal replicates: striatum 698, cortex 700, cerebellum 697, hippocampus 699, olfactory bulb 700, and hypothalamus 666.) The final column indicates those genes that are labeled as having present expression by present/absent calling algorithms for each platform minus those genes without consistent calls for those data available in replicate.

ISSN: 1474-760X