So a ballpark answer might be "at least 50 times harder".
The "at least" part seems wrong to me. Cellular differentiation works by deactivating some genes more-or-less permanently and by sequestering deactivated genes in densely packed regions of chromatin that are inaccessible to transcription complexes. (This is a one-sentence summary of an absurdly complex biological process. You have been warned.) Understanding the functional molecular biology of a highly differentiated cell type like a neuron won't require the understanding of 30K interacting genes.
Good point. Is anything known about what proportion of genes might be turned off in a differentiated cell?
"A Whole-Cell Computational Model Predicts Phenotype from Genotype" by Jonathan Karr et al.
This paper appeared a few days ago in Cell, and describes a computational simulation of the bacterium Mycoplasma genitalium, conducted at this lab. The paper is behind a paywall, but is blogged about here. The simulation software is freely available from the project web site.
From the abstract: "Here, we present a ‘‘whole-cell’’ model of the bacterium Mycoplasma genitalium, a human urogenital parasite whose genome contains 525 genes. Our model attempts to: (1) describe the life cycle of a single cell from the level of individual molecules and their interactions; (2) account for the specific function of every annotated gene product; and (3) accurately predict a wide range of observable cellular behaviors."
According to an editorial commentary in the same issue, this is the first simulation of a complete free-living microbe.