Biclustering of Expression Data

Yizong Cheng and George M. Church

Supplementary Information


Yeast expression matrix, based on Tavazoie et al. 8224 rows and 17 columns, 4 bytes for each element, with -1 indicating a missing value.
Human expression matrix, based on Alizadeh et al. with 4026 rows and 96 columns, 4 bytes for each element, and 999 indicating a missing value.
100 biclusters from the yeast data. Each bicluster is documented with three rows. The first row contains the number of rows, the number of columns, and the score. The second row is the column set and the third the row set. If a row index in the row set is preceded by a minus sign, the additive inverse was used in the process. All indices start at 0.
100 biclusters from the human data
Genes associated with rows of the yeast data
Comparison of the yeast biclusters and clusters in Tavazoie et al., After the index of each of the 100 biclusters, 30 numbers indicate the frequencies at which the elements occur in the 30 clusters of Tavazoie et al.
biclulym biclustering program executable on Solaris 7 for the human data. The user has to provide data filename and two thresholds (alpha in Algorithm 1 and delta in Algorithm 2) as command line arguments. To get the 100 biclusters listed above, use thresholds 1.2 and 1200. This version only works for the human data. Note: the program be renamed depending on your browser!
bcplot plotting program executable on Solaris 7 for the output of the previous program. Note: the program be renamed depending on your browser!