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Functionally related genes may be co-expressed only in a subset of conditions, and such gene sets would be missed by traditional clustering methods.
BEST is built under the hypothesis that the correlation between TF and its regulon only hold in a subset of conditions.
All four algorithms aim to find biclusters of genes with co-expression in a subset of conditions.
The other candidates from this sRNA class were detected only in a subset of conditions with the largest cluster comprising 19 candidates only found in a single condition.
Thus, the search can be guided directly towards the modules of interest, for example, modules that show coherent behavior in a subset of conditions.
However, the sets of edges within a gene covariation network can themselves vary from state to state, for example, when two genes are highly correlated in a subset of conditions but not across all conditions.
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Because the Dr Foster HSMR only focuses on in-hospital deaths for patients admitted with a subset of conditions, and in response to methodological concerns and transparency issues [ 9] a new measure - the Summary Hospital-Level Mortality Index (SHMI) – was developed.
One possibility explored by Sprouse and Cunningham (submitted for publication) was to plot the mean ratings of each condition in ascending order and identify a subset of conditions that appear to have a definitive rank order in the sample mean data.
In particular annotation terms specific for a subset of conditions could be identified, as well as annotation terms that are equally relevant for all the conditions.
To resolve this issue, a biclustering method can suitably substitute general clustering methods by providing correlated gene clusters under a subset of conditions in an unsupervised gene expression analysis.
In the example with CD4 T-lymphocytes, one of the genes was unlikely to be a good candidate as it responded strongly to a subset of conditions in the Conditions tool.
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