The most common function of proteins that contribute to pattern formation is that they are transcription factors, which control transcription.
Many tool kit genes are transcription factors.
Inspection of the Bicoid protein sequence shows that it has a homeodomain, which is distinct. So, Bicoid has the properties of a Deoxyribonucleic acid (DNA)-binding transcription factor.
In the same way, each gap gene encodes a transcription factor. For example, hunchback-zygotic and Kruppel genes encode transcription factor for zinc-ginger protein and knirps encodes for steroid receptor-type protein.
Each pair-rule gene encodes transcription factors. The even-skipped pair-rule gene encodes for transcription factor of the homeodomain protein and ftz encodes for both the homeodomain protein and odd-paired zinc-ginger protein.
Many segment-polarity genes and all the Hox genes encode transcription factors.
These transcription factors include representatives of many known families of sequence-specific DNA-binding proteins.
Some of the toolkit genes are components of signaling pathways. For example, wingless segment-polarity genes signal WG protein and hedgehog signals HH protein. The output of these pathways leads to gene activation or repression.
So, most toolkit proteins directly or indirectly affect gene regulation.