Genome Research scroll

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
 QUICK SEARCH:   [advanced]


     


This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Lai, C.-H.
Right arrow Articles by Lin, W.-c.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lai, C.-H.
Right arrow Articles by Lin, W.-c.
Right arrowPubmed/NCBI databases
*Gene*Genome
*GEO Profiles*Nucleotide
*OMIM*Protein
*UniGene*UniSTS
Social Bookmarking
 Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 10, Issue 5, 703-713, May 2000

METHODS
Identification of Novel Human Genes Evolutionarily Conserved in Caenorhabditis elegans by Comparative Proteomics

Chun-Hung Lai,1 Chang-Yuan Chou,1 Lan-Yang Ch'ang,1 Chung-Shyan Liu,2 and Wen-chang Lin1,3

1 Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China; 2 Department of Information Engineering, Chung Yuan C. University, Chung Li, Taiwan, Republic of China

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 GenBank data library under accession nos. AF132936-AF132973, AF151799-AF151909, and AF152097.]


3 Corresponding author.


10:703-713 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
haematolHome page
P. Rujkijyanont, K.-i. Watanabe, C. Ambekar, H. Wang, A. Schimmer, J. Beyene, and Y. Dror
SBDS-deficient cells undergo accelerated apoptosis through the Fas-pathway
Haematologica, March 1, 2008; 93(3): 363 - 371.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
R. Kairouz-Wahbe, H. Biliran, X. Luo, I. Khor, M. Wankell, C. Besch-Williford, J. Pascual, R. Oshima, and E. Ruoslahti
Anoikis effector Bit1 negatively regulates Erk activity
PNAS, February 5, 2008; 105(5): 1528 - 1532.
[Abstract] [Full Text] [PDF]


Home page
J. Cell Biol.Home page
K. Oishi, H. Okano, and H. Sawa
RMD-1, a novel microtubule-associated protein, functions in chromosome segregation in Caenorhabditis elegans
J. Cell Biol., December 17, 2007; 179(6): 1149 - 1162.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
N. Santama, S. C. Ogg, A. Malekkou, S. E. Zographos, K. Weis, and A. I. Lamond
Characterization of hCINAP, a Novel Coilin-interacting Protein Encoded by a Transcript from the Transcription Factor TAFIID32 Locus
J. Biol. Chem., October 28, 2005; 280(43): 36429 - 36441.
[Abstract] [Full Text] [PDF]


Home page
Physiol. GenomicsHome page
J. M. O. Fernandes, M. G. Mackenzie, G. Elgar, Y. Suzuki, S. Watabe, J. R. Kinghorn, and I. A. Johnston
A genomic approach to reveal novel genes associated with myotube formation in the model teleost, Takifugu rubripes
Physiol Genomics, August 11, 2005; 22(3): 327 - 338.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
L. Heiska and O. Carpen
Src Phosphorylates Ezrin at Tyrosine 477 and Induces a Phosphospecific Association between Ezrin and a Kelch-Repeat Protein Family Member
J. Biol. Chem., March 18, 2005; 280(11): 10244 - 10252.
[Abstract] [Full Text] [PDF]


Home page
GlycobiologyHome page
W. Chen, J. Tang, and P. Stanley
Suppressors of {alpha}(1,3)fucosylation identified by expression cloning in the LEC11B gain-of-function CHO mutant
Glycobiology, March 1, 2005; 15(3): 259 - 269.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
E. Lindersson, D. Lundvig, C. Petersen, P. Madsen, J. R. Nyengaard, P. Hojrup, T. Moos, D. Otzen, W.-P. Gai, P. C. Blumbergs, et al.
p25{alpha} Stimulates {alpha}-Synuclein Aggregation and Is Co-localized with Aggregated {alpha}-Synuclein in {alpha}-Synucleinopathies
J. Biol. Chem., February 18, 2005; 280(7): 5703 - 5715.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
H. Ren, L. Wang, M. Bennett, Y. Liang, X. Zheng, F. Lu, L. Li, J. Nan, M. Luo, S. Eriksson, et al.
The crystal structure of human adenylate kinase 6: An adenylate kinase localized to the cell nucleus
PNAS, January 11, 2005; 102(2): 303 - 308.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. Biol.Home page
G. Huang, H. Lu, A. Hao, D. C. H. Ng, S. Ponniah, K. Guo, C. Lufei, Q. Zeng, and X. Cao
GRIM-19, a Cell Death Regulatory Protein, Is Essential for Assembly and Function of Mitochondrial Complex I
Mol. Cell. Biol., October 1, 2004; 24(19): 8447 - 8456.
[Abstract] [Full Text] [PDF]


Home page
Physiol. Rev.Home page
C. A. Wagner, K. E. Finberg, S. Breton, V. Marshansky, D. Brown, and J. P. Geibel
Renal Vacuolar H+-ATPase
Physiol Rev, October 1, 2004; 84(4): 1263 - 1314.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
V. Subramanian, A. Rothenberg, C. Gomez, A. W. Cohen, A. Garcia, S. Bhattacharyya, L. Shapiro, G. Dolios, R. Wang, M. P. Lisanti, et al.
Perilipin A Mediates the Reversible Binding of CGI-58 to Lipid Droplets in 3T3-L1 Adipocytes
J. Biol. Chem., October 1, 2004; 279(40): 42062 - 42071.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
Y. Zhang, J. M. Foster, S. Kumar, M. Fougere, and C. K. S. Carlow
Cofactor-independent Phosphoglycerate Mutase Has an Essential Role in Caenorhabditis elegans and Is Conserved in Parasitic Nematodes
J. Biol. Chem., August 27, 2004; 279(35): 37185 - 37190.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
T. Yamaguchi, N. Omatsu, S. Matsushita, and T. Osumi
CGI-58 Interacts with Perilipin and Is Localized to Lipid Droplets: POSSIBLE INVOLVEMENT OF CGI-58 MISLOCALIZATION IN CHANARIN-DORFMAN SYNDROME
J. Biol. Chem., July 16, 2004; 279(29): 30490 - 30497.
[Abstract] [Full Text] [PDF]


Home page
Cancer Res.Home page
M. A. Olayioye, P. Hoffmann, T. Pomorski, J. Armes, R. J. Simpson, B. E. Kemp, G. J. Lindeman, and J. E. Visvader
The Phosphoprotein StarD10 Is Overexpressed in Breast Cancer and Cooperates with ErbB Receptors in Cellular Transformation
Cancer Res., May 15, 2004; 64(10): 3538 - 3544.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
P. Liu, Y. Ying, Y. Zhao, D. I. Mundy, M. Zhu, and R. G. W. Anderson
Chinese Hamster Ovary K2 Cell Lipid Droplets Appear to Be Metabolic Organelles Involved in Membrane Traffic
J. Biol. Chem., January 30, 2004; 279(5): 3787 - 3792.
[Abstract] [Full Text] [PDF]


Home page
J. Nutr.Home page
B. Kindermann, F. Doring, M. Pfaffl, and H. Daniel
Identification of Genes Responsive to Intracellular Zinc Depletion in the Human Colon Adenocarcinoma Cell Line HT-29
J. Nutr., January 1, 2004; 134(1): 57 - 62.
[Abstract] [Full Text] [PDF]


Home page
Genome Res.Home page
M. S. Clark, Y. J.K. Edwards, D. Peterson, S. W. Clifton, A. J. Thompson, M. Sasaki, Y. Suzuki, K. Kikuchi, S. Watabe, K. Kawakami, et al.
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
Genome Res., December 1, 2003; 13(12): 2747 - 2753.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. ProteomicsHome page
B. Knoblach, B. O. Keller, J. Groenendyk, S. Aldred, J. Zheng, B. D. Lemire, L. Li, and M. Michalak
ERp19 and ERp46, New Members of the Thioredoxin Family of Endoplasmic Reticulum Proteins
Mol. Cell. Proteomics, October 1, 2003; 2(10): 1104 - 1119.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
D. I. James, P. A. Parone, Y. Mattenberger, and J.-C. Martinou
hFis1, a Novel Component of the Mammalian Mitochondrial Fission Machinery
J. Biol. Chem., September 19, 2003; 278(38): 36373 - 36379.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
T. Hayano, M. Yanagida, Y. Yamauchi, T. Shinkawa, T. Isobe, and N. Takahashi
Proteomic Analysis of Human Nop56p-associated Pre-ribosomal Ribonucleoprotein Complexes: POSSIBLE LINK BETWEEN Nop56p AND THE NUCLEOLAR PROTEIN TREACLE RESPONSIBLE FOR TREACHER COLLINS SYNDROME
J. Biol. Chem., September 5, 2003; 278(36): 34309 - 34319.
[Abstract] [Full Text] [PDF]


Home page
J. Cell Sci.Home page
A. Mikami, S. H. Tynan, T. Hama, K. Luby-Phelps, T. Saito, J. E. Crandall, J. C. Besharse, and R. B. Vallee
Molecular structure of cytoplasmic dynein 2 and its distribution in neuronal and ciliated cells
J. Cell Sci., March 14, 2003; 115(24): 4801 - 4808.
[Abstract] [Full Text] [PDF]


Home page
Hum Mol GenetHome page
X. Estivill, J. Cheung, M. Angel Pujana, K. Nakabayashi, S. W. Scherer, and L.-C. Tsui
Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome
Hum. Mol. Genet., August 15, 2002; 11(17): 1987 - 1995.
[Abstract] [Full Text] [PDF]


Home page
Mol. Biol. CellHome page
P. M. Grissom, E. A. Vaisberg, and J. R. McIntosh
Identification of a Novel Light Intermediate Chain (D2LIC) for Mammalian Cytoplasmic Dynein 2
Mol. Biol. Cell, March 1, 2002; 13(3): 817 - 829.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. Biol.Home page
V. McCulloch, B. L. Seidel-Rogol, and G. S. Shadel
A Human Mitochondrial Transcription Factor Is Related to RNA Adenine Methyltransferases and Binds S-Adenosylmethionine
Mol. Cell. Biol., February 15, 2002; 22(4): 1116 - 1125.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
T. Nagaike, T. Suzuki, Y. Tomari, C. Takemoto-Hori, F. Negayama, K. Watanabe, and T. Ueda
Identification and Characterization of Mammalian Mitochondrial tRNA nucleotidyltransferases
J. Biol. Chem., October 19, 2001; 276(43): 40041 - 40049.
[Abstract] [Full Text] [PDF]


Home page
J Am Coll CardiolHome page
D.-S. Lim, R. Roberts, and A. J. Marian
Expression profiling of cardiac genes in human hypertrophic cardiomyopathy: insight into the pathogenesis of phenotypes
J. Am. Coll. Cardiol., October 1, 2001; 38(4): 1175 - 1180.
[Abstract] [Full Text] [PDF]


Home page
J. Virol.Home page
M. Huarte, J. J. Sanz-Ezquerro, F. Roncal, J. Ortin, and A. Nieto
PA Subunit from Influenza Virus Polymerase Complex Interacts with a Cellular Protein with Homology to a Family of Transcriptional Activators
J. Virol., September 15, 2001; 75(18): 8597 - 8604.
[Abstract] [Full Text] [PDF]


Home page
J. Cell Biol.Home page
S. Yamaji, A. Suzuki, Y. Sugiyama, Y.-i. Koide, M. Yoshida, H. Kanamori, H. Mohri, S. Ohno, and Y. Ishigatsubo
A Novel Integrin-linked Kinase-binding Protein, Affixin, Is Involved in the Early Stage of Cell-Substrate Interaction
J. Cell Biol., June 11, 2001; 153(6): 1251 - 1264.
[Abstract] [Full Text] [PDF]


Home page
Genome Res.Home page
K. Inoue, K. Dewar, N. Katsanis, L. T. Reiter, E. S. Lander, K. L. Devon, D. W. Wyman, J. R. Lupski, and B. Birren
The 1.4-Mb CMT1A Duplication/HNPP Deletion Genomic Region Reveals Unique Genome Architectural Features and Provides Insights into the Recent Evolution of New Genes
Genome Res., June 1, 2001; 11(6): 1018 - 1033.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
J. H. Heaton, W. M. Dlakic, M. Dlakic, and T. D. Gelehrter
Identification and cDNA Cloning of a Novel RNA-binding Protein That Interacts with the Cyclic Nucleotide-responsive Sequence in the Type-1 Plasminogen Activator Inhibitor mRNA
J. Biol. Chem., January 26, 2001; 276(5): 3341 - 3347.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
C. S. Moreno, W. S. Lane, and D. C. Pallas
A Mammalian Homolog of Yeast MOB1 Is Both a Member and a Putative Substrate of Striatin Family-Protein Phosphatase 2A Complexes
J. Biol. Chem., June 22, 2001; 276(26): 24253 - 24260.
[Abstract] [Full Text] [PDF]




Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.