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All the module genes are known to be mostly expressed in developing and mature B-cells, revealing a coherent module [27].
This is because the sample subgroup where the module genes are expressed is too small to be detected by the biclustering algorithm.
In the other model, bicluster model, module genes are assumed to be overexpressed in a subset of samples; since BEEM was developed to target this type of expression modules, BEEM shows the best performance for this model.
However, if the data contain heterogeneous transcriptome from a broad range of samples, an alternative would be more reasonable; module genes are assumed to be co-regulated in only a subset of samples.
The module genes are also enriched for binding of NDD1, an FKH2 transcriptional co-activator (Fig. 1b).
We next sought to use NEO to identify which of the module genes are directly downstream of Cd44.
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The 'blue' module genes were also enriched with ribonucleoprotein complex genes.
As shown above 16 of the 356 turquoise (4.5%) module genes were involved in oxphos.
An additional correctly inferred regulator of the muscle/glycolysis module genes is GLI1 [ 58].
The negative correlations reflect that most Yellow module genes were under-expressed in ALS patients.
In the former, high expression of module genes is detected primarily in highly dividing tissues.
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