Toward a Functional Annotation of the Human Genome Using Artificial Transcription Factors

Genome Res. 2003 Dec;13(12):2708-16. doi: 10.1101/gr.1397903.

Abstract

We have developed a novel, high-throughput approach to collecting randomly perturbed gene-expression profiles from the human genome.A human 293 cell library that stably expresses randomly chosen zinc-finger transcription factors was constructed, and the expression profile of each cell line was obtained using cDNA microarray technology.Gene expression profiles from a total of 132 cell lines were collected and analyzed by (1) a simple clustering method based on expression-profile similarity, and (2) the shortest-path analysis method. These analyses identified a number of gene groups, and further investigation revealed that the genes that were grouped together had close biological relationships. The artificial transcription factor-based random genome perturbation method thus provides a novel functional genomic tool for annotation and classification of genes in the human genome and those of many other organisms.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Antigens, Neoplasm / genetics
  • Antigens, Neoplasm / physiology
  • Cell Line
  • Computational Biology / methods*
  • Computational Biology / statistics & numerical data
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / physiology
  • Gene Expression Profiling / methods
  • Gene Expression Profiling / statistics & numerical data
  • Gene Expression Regulation / genetics
  • Genetic Linkage
  • Genome, Human*
  • Humans
  • Melanoma / genetics
  • Multigene Family
  • Oligonucleotide Array Sequence Analysis / methods
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Recombinant Proteins / analysis
  • Transcription Factors / genetics
  • Transcription Factors / physiology*
  • Zinc Fingers / genetics

Substances

  • Antigens, Neoplasm
  • DNA-Binding Proteins
  • Recombinant Proteins
  • Transcription Factors
  • SPIB protein, human