Graphics Reference
In-Depth Information
Matrix Visualization
of the KEGG Metabolism Pathway Data
15.7.2
he
Jaccarddistance coe
cient isusedtocomputetheproximitymatrices forboth
genes and pathways in Fig.
.
. Elliptical seriations (Chen,
) are employed to
permute the two
−
Jaccard distance matrices and the binary pathway data matrix.
One can easily see, from the binary data matrix map and the proximity matrix map
for genes, that there are many genes that are only involved in the activities of a single
pathway. We then exclude those genes from further analysis, since they provide no
association information. his reduces the original
genes by
pathways binary
matrix to a
genes by
pathways matrix (some pathways are also excluded ater
excluding genes). When there are too few horizontal or vertical pixels for an MV
−
Figure
.
.
Binary data matrix map for the Dataset
(KEGG metabolite pathway database with
genes (rows) for
pathways (columns)) with two Jaccard proximity matrices for genes and for
pathways sorted by elliptical seriations in both directions
