Home LiteratureArticle Details
PMID: 10810093 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics.

Genome research ·Vol. 10 ·No. 5 ·2000-05-00 ·Pages 703-13

Lai CH, Chou CY, Ch'ang LY, Liu CS, Lin W

Abstract

Modern biomedical research greatly benefits from large-scale genome-sequencing projects ranging from studies of viruses, bacteria, and yeast to multicellular organisms, like Caenorhabditis elegans. Comparative genomic studies offer a vast array of prospects for identification and functional annotation of human ortholog genes. We presented a novel comparative proteomic approach for assembling human gene contigs and assisting gene discovery. The C. elegans proteome was used as an alignment template to assist in novel human gene identification from human EST nucleotide databases. Among the available 18,452 C. elegans protein sequences, our results indicate that at least 83% (15,344 sequences) of C. elegans proteome has human homologous genes, with 7,954 records of C. elegans proteins matching known human gene transcripts. Only 11% or less of C. elegans proteome contains nematode-specific genes. We found that the remaining 7,390 sequences might lead to discoveries of novel human genes, and over 150 putative full-length human gene transcripts were assembled upon further database analyses. [The sequence data described in this paper have been submitted to the

MeSH Terms
Amino Acid Sequence Animals Base Sequence/genetics Caenorhabditis elegans/genetics Computational Biology Conserved Sequence/genetics Databases, Factual Evolution, Molecular Expressed Sequence Tags Genes, Helminth Humans Molecular Sequence Data Organ Specificity/genetics Proteome/genetics
Chemicals
Proteome
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Lai C H
Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China.
Chou C Y
Ch'ang L Y
Liu C S
Lin W
References (46)
46 references, click to expand
  1. The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics.
    Genome Res. 1999 Feb;9(2):195-209 PMID: 10022985
  2. Mining SNPs from EST databases.
    Genome Res. 1999 Feb;9(2):167-74 PMID: 10022981
  3. Detecting selective expression of genes and proteins.
    Genome Res. 1999 Mar;9(3):282-96 PMID: 10077535
  4. Reliable identification of large numbers of candidate SNPs from public EST data.
    Nat Genet. 1999 Mar;21(3):323-5 PMID: 10080189
  5. The complete family of genes encoding G proteins of Caenorhabditis elegans.
    Nat Genet. 1999 Apr;21(4):414-9 PMID: 10192394
  6. Characterization of single-nucleotide polymorphisms in coding regions of human genes.
    Nat Genet. 1999 Jul;22(3):231-8 PMID: 10391209
  7. Discovery of three novel orphan G-protein-coupled receptors.
    Genomics. 1999 Feb 15;56(1):12-21 PMID: 10036181
  8. The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes.
    Genome Res. 1999 Feb;9(2):103-20 PMID: 10022975
  9. An encyclopedia of mouse genes.
    Nat Genet. 1999 Feb;21(2):191-4 PMID: 9988271
  10. Human homologue of the Drosophila melanogaster lats tumour suppressor modulates CDC2 activity.
    Nat Genet. 1999 Feb;21(2):177-81 PMID: 9988268
  11. Small genes/gene-products in Escherichia coli K-12.
    FEMS Microbiol Lett. 1998 Dec 15;169(2):375-82 PMID: 9868784
  12. Comparison of the complete protein sets of worm and yeast: orthology and divergence.
    Science. 1998 Dec 11;282(5396):2022-8 PMID: 9851918
  13. Genome sequence of the nematode C. elegans: a platform for investigating biology.
    Science. 1998 Dec 11;282(5396):2012-8 PMID: 9851916
  14. Gene recognition by combination of several gene-finding programs.
    Bioinformatics. 1998;14(8):665-75 PMID: 9789092
  15. New goals for the U.S. Human Genome Project: 1998-2003.
    Science. 1998 Oct 23;282(5389):682-9 PMID: 9784121
  16. Protein-tyrosine kinase and protein-serine/threonine kinase expression in human gastric cancer cell lines.
    J Biomed Sci. 1998;5(2):101-10 PMID: 9662069
  17. Towards detection of orthologues in sequence databases.
    Bioinformatics. 1998;14(3):285-9 PMID: 9614272
  18. Analysis of EST-driven gene annotation in human genomic sequence.
    Genome Res. 1998 Apr;8(4):362-76 PMID: 9548972
  19. GeneFIND web server for protein family identification and information retrieval.
    Bioinformatics. 1998;14(2):223-4 PMID: 9545458
  20. Alternative gene form discovery and candidate gene selection from gene indexing projects.
    Genome Res. 1998 Mar;8(3):276-90 PMID: 9521931
  21. Identification and gene structure of a novel human PLZF-related transcription factor gene, TZFP.
    Biochem Biophys Res Commun. 1999 Nov 2;264(3):789-95 PMID: 10544010
  22. The human genome project: past, present, and future.
    Science. 1990 Apr 6;248(4951):44-9 PMID: 2181665
  23. Complementary DNA sequencing: expressed sequence tags and human genome project.
    Science. 1991 Jun 21;252(5013):1651-6 PMID: 2047873
  24. The complete DNA sequence of yeast chromosome III.
    Nature. 1992 May 7;357(6373):38-46 PMID: 1574125
  25. Identification of protein coding regions by database similarity search.
    Nat Genet. 1993 Mar;3(3):266-72 PMID: 8485583
  26. The human genome project.
    Proc Natl Acad Sci U S A. 1993 May 15;90(10):4338-44 PMID: 8506271
  27. dbEST--database for "expressed sequence tags".
    Nat Genet. 1993 Aug;4(4):332-3 PMID: 8401577
  28. A new five-year plan for the U.S. Human Genome Project.
    Science. 1993 Oct 1;262(5130):43-6 PMID: 8211127
  29. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
    Science. 1995 Jul 28;269(5223):496-512 PMID: 7542800
  30. ESTablishing a human transcript map.
    Nat Genet. 1995 Aug;10(4):369-71 PMID: 7670480
  31. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.
    Nature. 1995 Sep 28;377(6547 Suppl):3-174 PMID: 7566098
  32. The minimal gene complement of Mycoplasma genitalium.
    Science. 1995 Oct 20;270(5235):397-403 PMID: 7569993
  33. Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching.
    Nat Genet. 1996 Jun;13(2):167-74 PMID: 8640222
  34. The yeast genome project: what did we learn?
    Trends Genet. 1996 Jul;12(7):263-70 PMID: 8763498
  35. TDB: new databases for biological discovery.
    Methods Enzymol. 1996;266:27-40 PMID: 8743675
  36. Life with 6000 genes.
    Science. 1996 Oct 25;274(5287):546, 563-7 PMID: 8849441
  37. Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data.
    Genome Res. 1996 Sep;6(9):829-45 PMID: 8889550
  38. Identification through bioinformatics of two new macrophage proinflammatory human chemokines: MIP-3alpha and MIP-3beta.
    J Immunol. 1997 Feb 1;158(3):1033-6 PMID: 9013939
  39. Computational gene discovery and human disease.
    Curr Opin Genet Dev. 1997 Jun;7(3):416-23 PMID: 9229120
  40. Computational methods for the identification of genes in vertebrate genomic sequences.
    Hum Mol Genet. 1997;6(10):1735-44 PMID: 9300666
  41. Drosophila-related expressed sequences.
    Hum Mol Genet. 1997;6(10):1745-53 PMID: 9300667
  42. IMAGE cDNA clones, UniGene clustering, and ACeDB: an integrated resource for expressed sequence information.
    Genome Res. 1997 Oct;7(10):1027-32 PMID: 9331373
  43. A genomic perspective on protein families.
    Science. 1997 Oct 24;278(5338):631-7 PMID: 9381173
  44. Pieces of the puzzle: expressed sequence tags and the catalog of human genes.
    J Mol Med (Berl). 1997 Oct;75(10):694-8 PMID: 9382993
  45. Characterization of new proteins found by analysis of short open reading frames from the full yeast genome.
    Yeast. 1997 Nov;13(14):1363-74 PMID: 9392081
  46. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis.
    Genome Res. 1998 Mar;8(3):163-7 PMID: 9521918
Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.10.5.703
Published
2000-05-00
Pages
703-13
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC310876
Subset
IM
Databases
GENBANK
AF132936, AF132937, AF132938, AF132939, AF132940, AF132941, AF132942, AF132943, AF132944, AF132945, AF132946, AF132947, AF132948, AF132949, AF132950, AF132951, AF132952, AF132953, AF132954, AF132955, AF132956, AF132957, AF132958, AF132959, AF132960, AF132961, AF132962, AF132963, AF132964, AF132965
External Links
PubMed source DOI: 10.1101/gr.10.5.703 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2