| Category |
Symbol |
Definition of Symbol |
Number of
Subcases |
|
Genome Occurrence |
G(x) |
Number of times a particular PART occurs in genome x. (These are
based on PSI-blast comparisons between PDB and the genomes with an e-value
cutoff in these comparisons of .0001.) |
20 |
| Expression |
C(e) |
PART composition of the yeast transcriptome in expression level
experiment e. (Fold composition refers to the fraction of the mRNA population
with the fold. This is only applicable to expression experiments, such as
SAGE and GeneChips, that measure absolute mRNA levels in copies per cell.) |
8 |
| E(e) |
Transcriptome
enrichment compared to genome in experiment e. (Transcriptome enrichment is
defined as percentage difference the PART composition in the transcriptome and the genome. In symbols:
E(e) = [C(e)-G(Scer)] / G(Scer) .) |
8 |
| L(e) |
Average expression level of a particular PART. This is the average expression level over all genes that contain a this PART.
|
8 |
^M
| F(r) |
Expression
level fluctuation in experiment r. (This is the standard deviation in
expression level measurement over a timecourse.) |
7 |
| Alignments |
N(f) |
Number of aligned
pairs in pair-set f |
2 |
| U(f) |
RMS deviation
in Ca atoms averaged over all alignments in pair-set f |
2 |
| R(f) |
Similar to U(f)
for pair-set f but only the best fitting half of the atoms are included in
the calculation |
2 |
| S(f) |
Average
percentage identity between pairs of aligned proteins in pair-set f |
2 |
| P(f) |
Average sequence P-value for pair-set
f |
2 |
| Q(f) |
Average
structural P-value for pair-set f |
2 |
| Compositions |
B(a, p) |
Composition
of amino acid a in all structures in the PDB with this PART,
which is defined by p |
40 |
| motion
| M(s,d) |
The maximum value of statistic s
derived from surveying set of motions d in the Macromolecular Motions
Database for a particular PART,
where s is derived from all entries in the database that are associated with
the PART. |
7 |
| A(s,d) |
Similar to M(s,d) but now we
take the average instead of the maximum. |
7 |
| Interaction |
I(y,c) |
For a given PART, the number of types of
protein-protein interactions in interaction dataset y subject to the
restriction c regarding whether or not the proteins are on the same chain.
The number of interaction types is the number of distinctly different PART that interacts with a given PART. |
24 |
| J(y,c) |
For a given PART, the total number of types of interactions in interaction dataset y subject to the restriction c regarding whether or not the proteins are on the same chain. Here we show all interactions observed not just the number of distinct PART-PART interactions tabulated in I(y,c).
|
24 |
| Transposon |
T(b) |
The sensitivity
of the cell to transposon under different growth condition b. The sensitivity
was indicated by negative logarithm of P-value, which measures the degree to which the
observations for one particular gene could have resulted from wild-type cells
that randomly change their phenotype. |
20 |
| Miscelleneous |
X(q) |
Various miscellaneous
ranks |
5 |
| Total |
|
158 |
|
|
|
|