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For βF1, CγM1 and CLA expression, samples in which 30% or more of the cells expressed the antigen were scored as positive, as previously described.
The CK+ database (DB) is a set of facial expression samples posed by 123 people.
Where N is the number of expression samples, X is the expression level for gene X in ith sample, and Y is the expression level for gene Y in the ith sample (−1≤ r ≤1).
Here we describe DEGAS (DysrEgulated Gene set Analysis via Subnetworks), a new method for analysis of clinical gene expression samples in the context of interaction networks, which avoids the above assumption.
To investigate the kinetics of GrB expression, samples of culture supernatants were collected from methanol-induced cultures of pPIC9-GrB, pPIC9-GST-furS-GrB, or pPIC9-MBP-furS-GrB clones from day 1 to 4 after induction.
The remaining gene expression samples were further normalized as previously described for PA I.
This approach implicitly partitions the expression samples based on the modulator gene expression.
For each pair we computed their expression correlation using Kendall's Tau across the 314 expression samples.
After removing gene expression samples with unknown survival information, 427 samples were used in our analysis.
Expression samples were clustered hierarchically using all raw data (average linkage, uncentred Pearson correlation).
Consistent with the onset of AP expression, samples were collected at day 3.
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