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Table 2 Gene selection for ISH and microarray expression comparison

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

  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
  1. 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.