| Feature | Description
|
| Nuclear Localization Signal 1
| Four-residue patterns of
1. All basic amino acids (K or R) or
2. Three basic amino acids (K or R), and one H or P
(from-NK92).
|
| Nuclear Localization Signal 2
| Pattern starting with a P and followed within 3 residues by a basic 4-residue segment containing K or R residues (P.{0,3}[KR]{4}) (from-NK92).
|
| Mitochondrial Signal 1
| More than one N-terminal residue is cut (good chance of being mitochondrial).
|
| Mitochondrial Signal 2
| Mitochondrial matrix import sequence: The N-terminal of the protein has repeated alternating hydrophobic and hydrophilic patterns, and the protein contains at least 4 S or T residues in its 20 N-terminal residues.
|
| HDEL ER Retention Signal
| Endoplasmic reticulum retention signal (HDEL) (from-NK92). We checked for the presence of this signal in the 9 C-terminal residues.
|
| Plasma Membrane Signal
| Plasma membrane signal (from-NK92). We checked for this signal in the entire sequence, rather than just at the C-terminal.
|
| Peroxisome Import Signal
| C-terminal Peroxisome import signal ([SA][KRH]L) (from-NK92).
|
| Signal Sequence (method 1)
| Results of a simple program that predicts if a protein has a signal sequence. The pattern consists of a charged residue within the first seven residues, followed by a stretch of 14 residues with an average GES hydrophobicity less than -1 kcal/mole.
|
| Signal Sequence (method 2)
| Secretory signal peptide according to the SignalP server (Nielsen et al., 1997, 1999; von Heijne et al., 1997).
|
| Glycosylation sites
| Glycosylation site (from-NK92).
|
| Farnesylation site
| C-terminal farnesylation site: the sequence pattern consists of a Cysteine followed by two aliphatic residues and one more residue at the C-terminus (C[ALIVG][ALIVG].$) (Stryer, 1996).
|
| Geranylgeranylation site
| C-terminal geranylgeranylation site (CC$|C.C$|CC..$) (Stryer, 1996).
|
| Myristolation site
| N-terminal myristolation site :indicates that the protein may be a cytosolic protein anchored to the inside face of the plasma membrane. Consequently, its probability of inside goes up (Stryer, 1996).
|
| Potential CDC 28 kinase sites
| Potential cdc28 protein kinase sites.
|
| Potential Casein kinase II sites
| Potential casein kinase II protein kinase sites.
|
| Potential protein kinase A target sites
| Potential protein kinase A (cAMP-dependent protein kinase) target sites (from-MIPS).
|
| Coiled Coils
| Results of the Multicoil program that predicts the presence of coiled coils (from-MIPS) (Wolf et al., 1997).
|
| Young Absolute mRNA Expression
| Absolute mRNA expression in a GeneChip experiment (Holstege et al., 1998).
|
| SAGE Absolute mRNA Expression (g/m phase)
| Absolute mRNA expression of g/m phase proteins in the SAGE experiment (Velculescu et al., 1997).
|
| SAGE Absolute mRNA Expression (l phase)
| Absolute mRNA expression of l phase proteins in the SAGE experiment (Velculescu et al., 1997).
|
| SAGE Absolute mRNA Expression (s phase)
| Absolute mRNA expression of s phase proteins in the SAGE
experiment (Velculescu et al., 1997).
|
| Church Absolute mRNA Expression (a)
| Church Absolute mRNA Expression (a)
|
| Church Absolute mRNA Expression (alpha)
| Church Absolute mRNA Expression (alpha)
|
| Church Absolute mRNA Expression (gal)
| Church Absolute mRNA Expression (gal)
|
| Church Absolute mRNA Expression (heat)
| Church Absolute mRNA Expression (heat)
|
| Samson Absolute mRNA Expression
| Samson Absolute mRNA Expression
|
| Cell Cycle mRNA Expression Fluctuation (CDC15 arrest)
| Standard deviation in mRNA expression level over time (i.e. expression fluctuation) for a protein in the cdc15 arrest time series experiment in Yeast Cell Cycle Analysis Project (Spellman et al., 1998).
|
| Cell Cycle mRNA Expression Fluctuation (CDC28 arrest)
| Standard deviation in mRNA expression level over time (i.e. expression fluctuation) for a protein in the cdc28 time series experiment in Yeast Cell Cycle Analysis Project (Spellman et al., 1998).
|
| Cell Cycle mRNA Expression Fluctuation (Alpha-factor arrest)
| Standard deviation in mRNA expression level over time (i.e. expression fluctuation) for a protein in the Alpha-factor arrest time series experiment in Yeast Cell Cycle Analysis Project (Spellman et al., 1998).
|
| Cell Cycle mRNA Expression Fluctuation (Elutriation)
| Standard deviation in mRNA expression level over time (i.e. expression fluctuation) for a protein in the elutriation time series experiment in Yeast Cell Cycle Analysis Project (Spellman et al., 1998).
|
| Diauxic Shift mRNA Expression Fluctuation
| Standard deviation in mRNA expression level over time (i.e. expression fluctuation) for a protein in the diauxic shift experiment (DeRisi et al., 1997).
|
| Knockout Mutation
| Knockout mutation (lethal or viable). (from-MIPS) (Baudin et al., 1993; Shoemaker et al., 1996; Wach et al., 1994).
|
| Isoelectric Point
| pI (Isoelectric Point) values (from-MIPS).
|
| Trans-membrane Segments
| Results of a program that predicts whether a protein has transmembrane (TM) segments. TM segments were identified using the GES hydrophobicity scale (Engelman et al., 1986). The values from the scale for amino acids in a window of size 20 were averaged, and then compared against a cutoff value. We used the Boyd and Beckwith MaxH criteria to set the cutoffs as in previous analyses (Boyd et al., 1998; Klein et al., 1985; Gerstein et al., 2000).
|
| Length (amino acids)
| Length of a mature protein after the removal of N- and C- terminal peptides (from-MIPS).
|
| Surface Amino Acid Composition Compartment
| As given in the Andrade et al. paper, we calculated the two eigenvectors for all proteins using their surface amino acid compositions. We then plotted the proteins in the plane of the eigenvectors and divided the plane into 9 compartments, each of which served as a bin (Andrade et al., 1998; Rost & Sander, 1994).
|