Gene | F | ORE | N | Gene | F | ORE | N | Gene | F | ORE | N | Gene | F | ORE | N | Gene | F | ORE | N |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|

FAA2 | p | 1 | 31 | CMK1 | o | 6 | YGR243W | u | 3 | CAT8 | o | 1 | SMF2 | o | 1 | ||||

POX1 | p | 4 | 26 | IPT1 | p | 6 | YGR250C | o | 1 | 3 | CDA1 | o | 1 | TIF4631 | o | 1 | |||

ECI1 | p | 1 | 25 | MDH2 | p | 1 | 6 | YLR312C | u | 3 | CDC5 | o | 1 | WHI2 | o | 1 | |||

FOX2 | p | 1 | 25 | PEX5 | p | 6 | YMR041C | u | 3 | CYT1 | o | 1 | 1 | YAL053W | u | 1 | |||

TES1 | p | 1 | 25 | PEX6 | p | 1 | 6 | ACS2 | o | 1 | 2 | CYT2 | o | 1 | YDL085W | o | 1 | ||

PXA2 | p | 1 | 24 | RPN4 | o | 6 | AFG3 | o | 2 | DNM1 | o | 1 | YDL219W | o | 1 | ||||

SPS18 | o | 1 | 22 | SFC1 | o | 6 | ECM30 | o | 2 | ECM4 | o | 1 | YDR205W | o | 1 | ||||

IDP3 | p | 3 | 20 | SNF11 | o | 6 | GPX1 | o | 2 | ENB1 | o | 1 | YDR214W | u | 1 | ||||

PIP2 | p | 19 | ERG6 | p | 5 | GUT2 | o | 2 | ERF2 | o | 1 | YDR223W | u | 1 | |||||

POT1 | p | 2 | 18 | FUN34 | u | 5 | HMG1 | p | 2 | FRE1 | o | 1 | YDR247W | u | 1 | ||||

YLR287C | u | 17 | PEX14 | p | 5 | LYS9 | o | 2 | FSP2 | o | 1 | YGL101W | u | 1 | |||||

DCI1 | p | 15 | YIL060W | u | N/D | 5 | PDR15 | o | 2 | GAL11 | o | 1 | YHR054C | u | 1 | ||||

ECM13 | o | 14 | YPL112C | u | 1 | 5 | RIB1 | o | 2 | GDH3 | o | 1 | YHR080C | u | 1 | ||||

SPS19 | p | 1 | 14 | ARO9 | o | 4 | RIM11 | o | 2 | GDS1 | o | 1 | YHR132W-A | u | N/D | 1 | |||

YKR012C | u | N/D | 14 | CIT2 | p | 4 | RNC1 | o | 2 | GLG1 | o | 1 | YHR202W | u | 1 | ||||

CTA1 | p | 1 | 13 | EHT1 | o | 4 | YAT1 | p | 2 | HIR1 | o | 1 | YIL064W | u | 1 | ||||

ICL1 | p | 13 | FAT2 | p | 4 | YCR013C | u | N/D | 2 | INO1 | p | 1 | YIL163C | u | 1 | ||||

PEX15 | p | 1 | 13 | LYS1 | p | 4 | YDR036C | u | 2 | KNS1 | u | 1 | YJL112W | o | 1 | ||||

PEX18 | p | 1 | 13 | PEP1 | o | 4 | YER067W | u | N/D | 2 | LSM8 | o | 1 | YJL218W | u | 1 | |||

PSP1 | o | 13 | PEX13 | p | 2 | 4 | YFR011C | u | 2 | LYS14 | o | 1 | YJR120W | o | 1 | ||||

SPC25 | o | 1 | 13 | PXA1 | p | 1 | 4 | YGL196W | u | 2 | MCM1 | o | 1 | YKL054C | u | 1 | |||

YHR140W | u | 1 | 13 | RKI1 | o | 4 | YGR035C | u | 1 | 2 | MRF1 | o | 1 | YKR046C | u | 1 | |||

YMR018W | u | 13 | SAP155 | o | 4 | YIL057C | u | 2 | MRS6 | o | 1 | YKR064W | u | 1 | |||||

PEX1 | p | 1 | 12 | SDS23 | o | 4 | YJL217W | u | 2 | MSB1 | o | 1 | YLR294C | u | N/D | 1 | |||

YKR027W | u | 12 | YBR012C | u | 4 | YLR285W | u | 1 | 2 | MYO5 | o | 1 | YLR454W | u | 1 | ||||

YPL113C | u | 12 | YBR047W | u | 4 | YMR210W | u | 2 | NMD3 | o | 1 | YMR103C | u | 1 | |||||

YOR273C | o | 1 | 11 | YDR380W | u | 4 | YNL134C | u | 1 | 2 | NPL4 | o | 1 | YNL140C | u | N/D | 1 | ||

MLS1 | p | 10 | YEL020C | p | 4 | YOR086C | u | 2 | NRP1 | o | 1 | YNL144C | u | 1 | |||||

PEX11 | p | 1 | 10 | YHR056C | o | 4 | YOR138C | u | 2 | NUP145 | o | 1 | YNL205C | u | N/D | 1 | |||

YAP6 | o | 10 | YJR098C | u | 4 | YPL099C | u | 2 | NUP192 | o | 1 | YNL212W | u | 1 | |||||

YGR086C | u | 9 | YKL137W | o | 4 | YPL156C | u | 2 | OYE3 | p | 1 | 1 | YNL278W | u | 1 | ||||

YJL084C | u | 9 | YKL187C | u | 4 | YPL276W | u | 2 | PBI2 | o | 1 | YOL027C | u | 1 | 1 | ||||

CAT2 | p | 1 | 8 | YKR003W | p | 4 | YPL278C | u | 2 | PCA1 | o | 1 | YOL087C | u | 1 | ||||

MDH3 | p | 1 | 8 | YKR067W | p | 4 | YTA12 | o | 2 | PDE2 | o | 1 | YOR186W | u | 1 | ||||

YMR031C | u | 8 | ZTA1 | u | 4 | ADR1 | o | 1 | PDR12 | o | 1 | 1 | YOR240W | u | 1 | 1 | |||

YOR084W | u | 1 | 8 | CRC1 | p | 1 | 3 | AMS1 | o | 1 | PET9 | o | 1 | YPK2 | o | 1 | |||

YBL095W | u | 8 | HAP4 | o | 3 | ARG1 | o | 1 | PHO5 | o | 1 | YPL095C | u | 1 | 1 | ||||

GLN3 | o | 7 | ICL2 | o | 3 | ATP14 | o | 1 | PHO84 | o | 1 | YPL110C | u | 1 | 1 | ||||

PCL10 | o | 7 | LYS12 | o | 3 | ATP17 | o | 1 | PPA2 | o | 1 | YPL207W | u | N/D | 1 | ||||

SIP2 | u | 7 | NOS1 | o | 3 | ATP3 | o | 1 | PTC4 | o | 1 | YPL229W | u | 1 | |||||

YGR130C | u | 1 | 7 | NYV1 | o | 3 | ATP4 | o | 1 | RDI1 | o | 1 | YPL275W | u | 1 | ||||

YNR020C | u | 7 | QCR7 | o | 3 | ATP7 | o | 1 | REG2 | o | 1 | YPR003C | o | 1 | |||||

YOR087W | o | N/D | 7 | SNO1 | o | 3 | BNS1 | u | 1 | RPR2 | o | 1 | YPR117W | u | 1 | ||||

YPR023C | o | 7 | YDL110C | u | 3 | CAF17 | o | 1 | SEN1 | o | 1 | YPS1 | o | 1 | |||||

ARA1 | o | 6 | YFL030W | u | 3 | CAR2 | o | 1 | SKY1 | o | 1 | 1 |

The 224 candidate genes are listed. Column F contains functional classifications: p, genes having a role related to peroxisomes (i.e., involved in lipid, fatty acid, and sterol metabolism or encoding a protein that is either peroxisomal or a peroxin); o, genes with other cellular roles that have not been classified as “p”; u, unknown. Annotations are based on their classifications in the literature and in the Proteome database (Costanzo et al., 2000). Column ORE contains the number of OREs found upstream of each gene using ScanACE software (version 1.3) (Hughes et al., 2000a). Only elements that were <3 SDs from the motif average are reported. N/D, not determined. Column N contains the number of “hits” each gene received by all clustering methods. For a description of each “hit,” refer to the supplementary material. Two candidate genes of interest,

*YPL112c*(renamed PEX25) and*YOR084w*, are underlined.