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Table 2 Previously established definitions of four biological gold standards (GS) and the parameters of BLASTn results used in the theoretical predictions for identification of CSH probes (mouse probes used as an example).

From: In Silicocancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment

Gold Standard Parameters
GS1.x Top x ratio of relative expression (red/green) when exposed to erroneous RNA vs to correct RNA:
GS2.x* Top x% absolute expression when exposed to human RNA with mouse probes
GS3.x Top x% relative expression when exposed to human RNA with mouse probes (the expression of mouse probes when exposed to human RNA divided by the expression when exposed to mouse RNA)
GS4.x The same as GS2 but absolute log2 based expression on both green channels of human and mouse RNA expression of mouse probes > 4
Models Conditions and parameters
Model1* {18<Align≤20 and mis<5} U {20<Align≤ 30 and mis<6} U {30<Align≤40 and mis<7} U {40<Align≤50 and mis<8} U {50<Align and mis<9}
Model2 {15 < Align ≤ 30 and mis < 2} U {30 < Align ≤ 40 and mis < 3} U {40 < Align ≤ 50 and mis < 5} U {50< Align and mis < 7}
Model3 Alig > 50 & mismatches < 6
Model4 score > 70 & Alig > 58 & mis < 6
  1. Legend: biological GS: biological gold standard; CSH: cross-species hybridization; Align: alignment; mis: mismatch; U: union.
  2. The Gold Standards used in the final design are annotated with an asterisks (*). These were selected by comparing the initial biological experimental data and BLAST predictions using H&M array version 1.0 and details of this section are provided in our previous publication [17].