Concluding a DecCor2 Session

Pressing the “OK” button in the lower right-hand corner exits the graphic
display portion of DecCor2 and initiates the creation of the output fi le. This
output fi le will be created in the directory containing the DecCor2 executable
and will have the name specifi ed by the user during program initialization.
This output fi le, which should be opened in a text editor such as Wordpad that
supports long lines, consists of three portions:
1. A series of 200 bins containing the counts of correlation coeffi cients falling
within each bin. Suitable for constructing a histogram of the global distribution
of correlation coeffi cients, this output often assumes a very normal appearance
when using a large input data set.
2. A rowwise output of all the input genes, followed by a list on the same row of
all the genes that had a correlation coeffi cient higher than the specifi ed number
of SDs above the mean of all the pairwise correlation coeffi cients. The cutoff
correlation coeffi cient used for this output is the aforementioned global cutoff.
3. Another rowwise list of all genes, followed by a list on the same row of all the
genes with a correlation coeffi cient exceeding a gene-specifi c cutoff. In this
case, the cutoff is the mean plus the specifi ed number of SDs calculated from the
distribution of only that gene’s pairwise correlation coeffi cients. Optionally, this
list may be fi ltered to show only genes that are pairwise reciprocal (i.e., GeneB
appears in the list for GeneA, and vice versa). Both of the gene lists generated are
intended to help identify genes that are most similar in their pattern of expression
to the gene listed in the fi rst column. Note that the most similar gene is always
itself, owing to the correlation coeffi cient of 1 for self-similarity.