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Figure 2 | Plant Methods

Figure 2

From: SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea

Figure 2

ER3 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).

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