Basic Features in Three Genome-Wide Expression Experiments
| References | Roth et al.(1998) | Cho et al. (1998) | Spellman et al. (1998) |
| Goals | Gal-responsive, heat shock and mating type-specific genes and cis-acting elements | Cell cycle-regulated genes and cis-acting elements | Cell cycle-regulated genes and cis-acting elements |
| Technology | Affymetrix oligo chips | Affymetrix oligo chips | cDNA microarrays |
| Experiments and synchronization methods | two-point comparisons: (1) galactose vs. glucose; (2) 39°C vs. 30°C; (3) type α vs. typea | multipoint comparisons: (1) cdc28-13 ts mutant;[i] (2) cdc15-2 ts mutant | two-point comparisons: (1) cln3+ vs.cln3− ; (2) clb2+ vs.clb2− ; |
| Multipoint comparisons: (1) α-factor arrest; (2) elutriation; (3)cdc15-2 ts mutant | |||
| Cluster methods | simple sorting | visual identification of periodic peaks | simple sorting for the two-point data; Fourier transform and Pearson-type correlation for the multipoint |
| Putative new/total genes identified | (1) 3/9, (2) 6/33, (3) 7/40 | ∼300/416 | ∼700/800 |
| Motif tools | AlignACE | oligonucleotide bias | oligonucleotide information |
| Database search | TRANSFAC | visual extension | GibbsDNA |
| TRANSFAC | TRANSFAC+SCPD | ||
| Upstream of ATG | <600 bp | 500 bp | 700 bp |
[i] (ts) Temperature sensitive.