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Bioinformatics was born somewhere between the “old” and “new” biology
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It’s hard to be an expert on 25,000+ genes
In molecular biology cleverness is finding a way to answer a question definitively by ignoring 99.99% of genes.  You can’t see them, so the experiment must exclude them.
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Controls & stats – if you want to see what genes are changing on a microarray, you should have some controls – those you expect should change and those that shouldn’t
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However, it is becoming clear that we need to reverse the process, and to study how these components interact to form complex systems. 
This poses the question, given the complete genomic sequence, is it possible to reconstruct the functions of a cellular or biological system. 
The process of reconstructing the biological system from the reductionist information will rely on bioinformatics to identify the “parts catalogue” if you will. 
However, the parts catalogue does not contain functional information.  for example, listing all the parts of car, does not even begin to describe the how the  the automobile works. 
Therefore, to understand multigenic functions, a systems science analysis is required.