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Functional Analysis Program

Researcher, microarray


Functional Analysis Program Overview

Completely sequencing an organism's genome is just the beginning of our understanding of that organism's biology. All of the genes still need to be identified; the function of those genes' expressed products (functional RNAs and proteins) must be elucidated; and the non-coding regulatory sequences need to be understood. The Functional Analysis of the Genome program manages and supports research that will lead to improved techniques and strategies for efficient identification and functional analysis of genes, coding regions and other functional elements of entire genomes on a high throughput basis.

The main emphasis of this program is technology development. These technologies must be efficient, robust and have the potential to be applied in a large-scale yet cost-effective manner. The program also supports the large-scale application of high-throughput and efficient technologies on a limited basis, primarily in model organisms. (The application of these technologies to specific, highly focused biological or medical problems is not supported under this program).

Functional Analysis Program Research Objectives:

  • Identification and mapping of all functional elements (both coding and non-coding) in a genome.
  • Generation of high-quality, full-length and representative cDNA libraries.
  • Analysis of steady-state RNA and protein expression levels in a given cell type; of comparative levels of gene products in different cell types; and of temporal or induced changes in RNA and protein expression.
  • Analysis of naturally occurring or induced mutations that alter RNA and/or protein expression.
  • Analysis of cellular localization of proteins and of protein-protein, or protein-nucleic acid, interactions.
  • Comparative analysis of protein sequences.
  • Analysis of genome organization and its effect on cellular functions.


Functional Analysis Program Policies, Reports and Related Program Information

Workshop Reports

Workshop on the Comprehensive Extraction of Biological Information from Genomic Sequence July 23 - 24, 2002

Non-Mammalian Models Workshop [nih.gov] February 16-17, 1999

Functional Analysis Workshop December 2-3, 1997

Related Projects

ENCODE (Encyclopedia of DNA Elements)
The long-term goal of the ENCODE project is to identify all functional elements in the human genome sequence. For use in a pilot project, defined regions of the human genome - corresponding to 30Mb, roughly 1 percent - have been selected. These regions will serve as the foundation on which to test and evaluate the effectiveness and efficiency of a diverse set of methods and technologies for finding various functional elements in human DNA.

Full-length cDNA Project (The Mammalian Gene Collection) [mgc.nci.nih.gov]
The goal of the Mammalian Gene Collection (MGC) project is to identify, sequence and make available to the research community, one representative, full-length (full open reading frame) clone for every human and mouse gene. The MGC website provides information about the confirmed, full ORF clones and cDNA libraries, and describes how to access the resources. The MGC is a trans-National Institutes of Health (NIH) initiative co-led by the National Human Genome Research Institute (NHGRI) and the National Cancer Institute (NCI).

Model Organisms for Biomedical Research [nih.gov]
Provides information and relevant links for trans-NIH model organism initiatives and their related funding opportunities.


NHGRI Rapid Data Release Policy (January 2003)

NIH-DOE Guidelines for Access to Mapping and Sequencing Data and Material Resources (Spring 1998)

For additional information regarding data release for large-scale sequencing of model organism genomes, see: Guyer, M. Statement on the Rapid Release of Genomic DNA Sequence. Genome Research, 8(5): 413. 1998. [Full Text]


Functional Analysis Program Funding Opportunities

  • Technology Development for High-Throughput Functional Genomics (R01)
    RFA-HG-11-013 [grants.nih.gov]
    Application Receipt Date(s): August 2, 2011
  • Technology Development for High-Throughput Functional Genomics (R21)
    RFA-HG-11-014 [grants.nih.gov]
    Application Receipt Date(s): August 2, 2011
  • Technology Development for High-Throughput Functional Genomics (R43/44)
    RFA-HG-11-015 [grants.nih.gov]
    Application Receipt Date(s): August 2, 2011

Archival: PA-97-044: Technologies for Genomic Mapping, Sequencing and Analysis [Expired]
This announcement solicited investigator-initiated proposals to develop new technologies.

Centers of Excellence in Genomic Science (CEGS)

Expired Grant Solicitations

Functional Analysis Program Staff

Program Directors

Elise Feingold, Ph.D.
E-mail: feingole@exchange.nih.gov

Bettie Graham, Ph.D.
E-mail: grahamb@nhgri.nih.gov

Michael Pazin, Ph.D.
E-mail: pazinm@mail.nih.gov

Program Analysts

Sherry Zhou
E-mail: xiao-qiao.zhou@nih.gov

Last updated: March 16, 2012