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336 IndexKknockin (gene knockin) 193, 211–212knockout (gene knockout) 1–2, 6, 13,193–194, 196–198, 200–201, 203,206, 208, 244Llibrary (cDNA) 194, 258, 261, 269, 292ligand 71, 89Mmatrix (mathematical) 1, 4–5, 8–10, 12,35–36, 38–41, 45, 102, 138–139, 142,144, 177–178, 180Oortholog 23–24, 93–96, 98–99, 101,103–104, 132–141, 145, 196Pparalog 93–94, 103, 124pathway 1, 5, 11, 13, 15, 17, 19–20,27–28, 50, 64, 71, 109–110, 119, 121,174, 283, 289phage displayantibody phage display 243–244phenotype 1–2, 15, 19, 24, 50, 171–175,177–179, 188, 193–194, 196, 208,211, 244, 260, 265–266, 276–277,282, 284, 288, 305, 309, 311–312phylogenetic footprinting (or profiling)109–110, 112, 116, 125, 130–131,134–135polymorphism 194, 202, 232primer 197–205, 208, 214–216, 218, 227,234–236, 263–264, 279–282, 287–288,301, 310, 314, 318, 324, 328, 332promoter analysisprotein complex 17, 194, 224protein interaction map 110, 228protein-DNA interaction 51, 131, 319TF-DNA interaction 129, 132, 134protein-protein interaction 51, 109, 257,288–289, 291–292, 296Rrecombination 281, 283, 288, 290, 312,324–326homologous recombination 193, 202regulatory network 20, 49–51, 55, 64,129–130reporterauxotrophic 263, 266, 276–277,294–295, 303, 312bacterial reporter 295, 304–305BacteriomatchII 295, 301, 303colorimetric 258, 266, 276–277,287, 294, 303LacZ or GasA 260–262, 267–268,284, 294–295, 312HIS3/aadA 294–295, 303,319–320, 325RISC (RNA-induced silencingcomplex) 224RNAmRNA 35–36, 38, 195, 211–212, 215,217, 243siRNA 2, 223–226, 230, 232, 236shRNA 211–221, 223–231,233–239shRNA-resistant cDNA 211,217, 219SSAGE (serial analysis of gene expression)194–195, 200Sequence Analysis 78, 133, 315BLAST (Basic Local AlignmentSearch Tool) 96–100, 102–104,111–118, 121, 124–126,194–196, 233ClustalW 99, 103FASTA format 55, 60, 78, 81, 85,113, 196position weight matrix (PWM) 51,130–135, 141, 145silent mutation 211–212, 217Statisticscorrelation coefficient 175, 182