Regulatory Elements Identified in Expression Clusters
| Sequence | Frequency | K-means cluster | Potential function of genes with sequence elements | Pvalue | Potential binding factor | Consensus | Refs |
| GTGGCAAA | 27/281 | V | Ubiquitin-dependent protein degradation | 1.2 × 10−11 | RPN4 | GGTGGCAA | (Jelinsky et al. 2000; Mannhaupt et al. 1999) |
| AAAATTTT | 173/435 | XVIII | Nucleolus/transcription from pol I promoter | 5.9 × 10−38 | Unknown | Unknown | |
| GCGATGAG | 47/435 | XVIII | Nucleolus/transcription from pol I promoter | 3.6 × 10−23 | Unknown | Unknown | |
| TCCGTACA | 28/435 | XVIII | Cytosolic ribosome | 9.9 × 10−18 | RAP1 | Unknown | (Kurtz and Shore 1991; Moehle and Hinnebusch 1991) |
| CCAATCA | 23/170 | XVI | Hydrogen/energy transport | 1.2 × 10−9 | HAP2 | CCAAT | (Ozsarac et al. 1997) |
| VAAAGGG | 30/303 | XI | Unknown | 1.1 × 10−11 | Unknown | Unknown |
[i] The sequence GTGGCAAA was overrepresented upstream of genes in the cluster containing genes with a potential functional role in the 26S proteosome. This sequence is the consensus-binding site for Rpn4p, a key regulator of proteosome function, and it is found in a number of genes involved in protein degradation (Mannhaupt et al. 1999). The sequence CCAATCA was overrepresented upstream of genes in the cluster of genes, along with hydrogen-transporting ATP synthase genes that have a putative mitochondrial function. This sequence contains the consensus HAP2 binding-site CCAAT(Ozsarac et al. 1997).
[ii] ATP, adenosine triphosphate.