Hox genes act as master switches, turning on and off other genes during embryonic development ensuring that organs and other body parts form in their proper place and time in the developing animal. They encode a protein that binds DNA to regulate gene expression by binding homeobox sequences upstream of the gene.
As master mapping genes the Hox gene family controls the regional placements of each embryonic cell as it appears, and what its identity and purpose in life will be. These Hox proteins co-act with regional, or organ specific, regulatory proteins to direct the fate of every cell’s future course in life. Hox body pattern regulation evolved because some patterns of grouping cells were more efficient than others.
So one set of Hox genes will say this is the head to tail axis, in a set order: head, cervical, thorax, abdomen, & caudal (tail) zone. Another Hox set maps back to front. Another set maps center (median) of the body out to the distal tips of extremities to map the bilateral limbs. Now in each zone are proteins for specialization of cells in the head now that the head end is defined. These preset the cells that will become the eye when it is time. Another set of proteins group together to regulate that these cells will be the brain.
Cells are set up in zones of potential growth in their correct time by combinations of regulatory proteins. The regulatory proteins sit on the strands of DNA to control what more proteins get expressed at the next level of development.
The final result is a hierarchic ranks of regulation:
1 Hox mapping regulation proteins. Whole body axis planers.
2 Master body specialist location/organ regulators (master contractors that oversee organ construction). Eye, limb bud, heart. Look up Pax6, Dll, Tinman for examples of DNA binding regulatory proteins that focus the local organ or limb organization during development. Those homeobox genes are capable of homeotic transformations are a subset of the Hox gene family that maps the body axes.
3 Regulators at the cell level to keep the life process going. Cellular housekeeping genes for cellular functions common to all cell based life
Hox code for humans - http://scienceblogs.com/pharyngula/2007/09/the_hox_code.php
Hox overview - http://www.pharyngula.org/index/weblog/comments/a_brief_overview_of_hox_genes/
Concepts of Hox function - http://pharyngula.org/index/weblog/comments/exorcising_hox/P25/