Human Genome Project
U.S. Department of Energy

HGP Research Area: Comparative and Functional Genomics

An important aspect of the HGP was functional and comparative genomics.

Functional Genomics

Understanding the function of genes and other parts of the genome is known as functional genomics. Sequencing the genome was just the first step in understanding humans at the molecular level. Though the sequencing phase of the project is complete, work is ongoing to determine the function of many human genes.

Efficient interpretation of the functions of human genes and other DNA sequences requires that resources and strategies be developed to enable large-scale investigations across whole genomes. A technically challenging first priority is to generate complete sets of full-length cDNA clones and sequences for human and model-organism genes. Other functional genomics goals include studies into gene expression and control, creation of mutations that cause loss or alteration of function in nonhuman organisms, and development of experimental and computational methods for protein analyses.

Functional Genomics Technology Goals

  • Generate sets of full-length cDNA clones and sequences that represent human genes and model organisms.
  • Support research on methods for studying functions of nonprotein-coding sequences.
  • Develop technology for comprehensive analysis of gene expression.
  • Improve methods for genome-wide mutagenesis.
  • Develop technology for large-scale protein analyses.

Comparative Genomics

The functions of human genes and other DNA regions often are revealed by studying their parallels in nonhumans. To enable such comparisons, HGP researchers have obtained complete genomic sequences for the bacterium Escherichia coli, the yeast Saccharomyces cerevisiae, the roundworm Caenorhabditis elegans, the fruitfly Drosophila melanogaster, the laboratory mouse, and many other organisms. The availability of complete genome sequences generated both inside and outside the HGP is driving a major breakthrough in fundamental biology as scientists compare entire genomes to gain new insights into evolutionary, biochemical, genetic, metabolic, and physiological pathways.

Comparative Genomics Goals

  • Complete the sequence of the roundworm C. elegans genome by 1998.
  • Complete the sequence of the fruitfly Drosophila genome by 2002.
  • Develop an integrated physical and genetic map for the mouse, generate additional mouse cDNA resources, and complete the sequence of the mouse genome by 2008.
  • Identify other useful model organisms and support appropriate genomic studies.

Completion Dates of All Functional & Comparative Genomics Goals

AreaHGP GoalStandard AchievedDate Achieved
Functional AnalysisDevelop genomic-scale technologiesHigh-throughput oligonucleotide synthesis1994
Functional AnalysisDevelop genomic-scale technologiesDNA microarrays1996
Functional AnalysisDevelop genomic-scale technologiesEukaryotic, whole-genome knockouts (yeast)1999
Functional AnalysisDevelop genomic-scale technologiesScale-up of two-hybrid system for protein-protein interaction2002
Gene IdentificationFull-length human cDNAs15,000 full-length human cDNAsMarch 2003
Model OrganismsComplete genome sequences of E. coliS. cerevisiaeC. elegansD. melanogasterFinished genome sequences of E. coliS. cerevisiaeC. elegansD. melanogaster, plus whole-genome drafts of several others, including C. briggsae, D. pseudoobscura, mouse, and ratApril 2003

Text adapted from F. Collins, Ari Patrinos, et al., “New Goals for the U.S. Human Genome Project: 1998-2003,” Science 282: 682-689 (1998). See HGP Goals for more details.


  • Functional Genomics abstracts from 2002 U.S. DOE Human Genome Program Contractor-Grantee Workshop IX
  • Functional Genomics abstracts from 2000 U.S. DOE Human Genome Program Contractor-Grantee Workshop VIII
  • Abstracts from the 1999 U.S. DOE Human Genome Program Contractor-Grantee Workshop VII
  • Abstracts from Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis 10th Annual Workshop October 28 through October 31, 2000
  • Abstracts from Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis 9th Annual Workshop, October 28-31, 1999
  • Abstracts from Identification of Transcribed Sequences: Functional and Expression Analysis: November 1997
  • Abstracts from 6th International Workshop on the Identification of Transcribed Sequences October 3-5, 1996

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