TY - JOUR
T1 - Gene index analysis of the human genome estimates approximately 120,000 genes
AU - Liang, Feng
AU - Holt, Ingeborg
AU - Pertea, Geo
AU - Karamycheva, Svetlana
AU - Salzberg, Steven L.
AU - Quackenbush, John
N1 - Funding Information:
We thank the remaining members of the TIGR Gene Index Team, T. Hansen and J. Upton; A. Glodek for database development efforts; M. Heaney and S. Lo for database support; V. Sapiro, B. Lee, S. Gregory, R. Karamchedu, C. Irwin, L. Fu and E. Arnold for computer system support; and C. Ronning, R. Buell, J. White, and C.M. Fraser for thoughtful comments and suggestions. This work was supported by a grant from the U.S. Department of Energy.
PY - 2000/6
Y1 - 2000/6
N2 - Although sequencing of the human genome will soon be completed, gene identification and annotation remains a challenge. Early estimates suggested that there might be 60,000-100,000 (ref. 1) human genes, but recent analyses of the available data from EST sequencing projects have estimated as few as 45,000 (ref. 2) or as many as 140,000 (ref. 3) distinct genes. The Chromosome 22 Sequencing Consortium estimated a minimum of 45,000 genes based on their annotation of the complete chromosome, although their data suggests there may be additional genes4. The nearly 2,000,000 human ESTs in dbEST provide an important resource for gene identification and genome annotation, but these single-pass sequences must be carefully analysed to remove contaminating sequences, including those from genomic DNA, spurious transcription, and vector and bacterial sequences. We have developed a highly refined and rigorously tested protocol for cleaning, clustering and assembling EST sequences to produce high-fidelity consensus sequences for the represented genes (F.L. et al., manuscript submitted) and used this to create the TIGR Gene Indices5—databases of expressed genes for human, mouse, rat and other species (http://www.tigr.org/tdb/tgi.html). Using highly refined and tested algorithms for EST analysis, we have arrived at two independent estimates indicating the human genome contains approximately 120,000 genes.
AB - Although sequencing of the human genome will soon be completed, gene identification and annotation remains a challenge. Early estimates suggested that there might be 60,000-100,000 (ref. 1) human genes, but recent analyses of the available data from EST sequencing projects have estimated as few as 45,000 (ref. 2) or as many as 140,000 (ref. 3) distinct genes. The Chromosome 22 Sequencing Consortium estimated a minimum of 45,000 genes based on their annotation of the complete chromosome, although their data suggests there may be additional genes4. The nearly 2,000,000 human ESTs in dbEST provide an important resource for gene identification and genome annotation, but these single-pass sequences must be carefully analysed to remove contaminating sequences, including those from genomic DNA, spurious transcription, and vector and bacterial sequences. We have developed a highly refined and rigorously tested protocol for cleaning, clustering and assembling EST sequences to produce high-fidelity consensus sequences for the represented genes (F.L. et al., manuscript submitted) and used this to create the TIGR Gene Indices5—databases of expressed genes for human, mouse, rat and other species (http://www.tigr.org/tdb/tgi.html). Using highly refined and tested algorithms for EST analysis, we have arrived at two independent estimates indicating the human genome contains approximately 120,000 genes.
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U2 - 10.1038/76126
DO - 10.1038/76126
M3 - Article
C2 - 10835646
AN - SCOPUS:0034204044
SN - 1061-4036
VL - 25
SP - 239
EP - 240
JO - Nature genetics
JF - Nature genetics
IS - 2
ER -