Figure 2From: SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpeaER3 versus inverse ER2 plot produced by SSHscreen for the cowpea forward (a) and reverse (b) libraries. (a) ER3 for the forward library was calculated as the log-2 ratio of the unsubtracted treated cDNA (UT; drought stressed sample) divided by the unsubtracted control cDNA (UC). Inverse ER2 was calculated as the log-2 ratio of UT divided by the subtracted treated cDNA (ST; SSH library enriched for genes up-regulated by drought stress). Data points were classified as representing transcripts: up-regulated by stress treatment/rare (Up.Rare: quadrant 1; ER3 > 0 and inverse ER2 < 0); up-regulated by stress treatment/abundant (Up.Abundant: quadrant 2; ER3 > 0 and inverse ER2 > 0); down-regulated by stress treatment/rare (Down.Rare: quadrant 3; ER3 < 0 and inverse ER2 > 0); and down-regulated by stress treatment/abundant (Down.Abundant: quadrant 4; ER3 < 0 and inverse ER2 < 0). The top 300 statistically significant clones are represented on the plot (adjusted p value < 0.05). (b) ER3 for the reverse library was calculated as the log-2 ratio of the unsubtracted control cDNA (UC) divided by the unsubtracted treated cDNA (UT; drought stressed). Inverse ER2 was calculated as the log-2 ratio of the unsubtracted control cDNA (UC) divided by the subtracted control cDNA (SC; SSH library enriched for genes down-regulated by drought stress). Data points were classified as representing transcripts: down-regulated by stress treatment/rare (Down.Rare: quadrant 1; ER3 > 0 and inverse ER2 < 0); down-regulated by stress treatment/abundant (Down.Abundant: quadrant 2; ER3 > 0 and inverse ER2 > 0); up-regulated by stress treatment/rare (Up.Rare: quadrant 3; ER3 < 0 and inverse ER2 > 0); and up-regulated by stress treatment/abundant (Up.Abundant: quadrant 4; ER3 < 0 and inverse ER2 < 0). The top 300 statistically significant clones are represented on the plot (adjusted p value < 0.05).Back to article page