Heart-specific genes revealed by expressed sequence tag (EST) sampling

Genome Biology

Volumn 3, Issue 12, 2002, Pages

  Mégy, Karine ^a   Audic, Stéphane ^a   Claverie, Jean Michel ^a  

^a CNRS   (France)

Author keywords

Biomedical Interest; Cardiac Gene; Core Promoter Region; Eukaryotic Promoter Database; Human Genome Sequence

Indexed keywords

ADULT; ANTIBODY SPECIFICITY; ARTICLE; CHEMISTRY; CHROMOSOME MAP; CLUSTER ANALYSIS; COMPARATIVE STUDY; CONTIG MAPPING; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC DATABASE; GENETICS; HEART DISEASE; HEART MUSCLE; HUMAN; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROMOTER REGION; STATISTICS; VASCULAR SMOOTH MUSCLE;

ADULT; CHROMOSOME MAPPING; CLUSTER ANALYSIS; CONTIG MAPPING; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; HEART DISEASES; HUMANS; MUSCLE, SMOOTH, VASCULAR; MYOCARDIUM; ORGAN SPECIFICITY; PROMOTER REGIONS (GENETICS);

EID: 0038652123     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2002-3-12-research0074     Document Type: Article

References (37)

1. Claverie JM: Computational methods for the identification of differential and coordinated gene expression. Hum Mol Genet. 1999, 8: 1821-1832. 10.1093/hmg/8.10.1821. DOI: 10.1093/hmg/8.10.1821
2. Brazma A, Jonassen I, Vilo J, Ukkonen E: Predicting gene regulatory elements in silico on a genomic scale. Genome Res. 1998, 8: 1202-1215.
3. Anderson L, Seilhamer J: A comparison of selected mRNA and protein abundances in human liver. Electrophoresis. 1997, 18: 533-537. DOI: 10.1002/elps.1150180333
4. Gygi SP, Rochon Y, Franza BR, Aebersold R: Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999, 19: 1720-1730. DOI: 10.1128/MCB.19.3.1720
5. Kurian KM, Watson CJ, Wyllie AH: DNA chip technology. J Pathol. 1999, 187: 267-271. 10.1002/(SICI)1096-9896(199902)187:3<267::AID-PATH275>3.3.CO;2-R. DOI: 10.1002/(SICI)1096-9896(199902)187:3<267::AID-PATH275>3.0.CO;2-#
6. Okubo K, Hori N, Matoba R, Niiyama T, Fukushima A, Kojima Y, Matsubara K: Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nat Genet. 1992, 2: 173-179. DOI: 10.1038/ng1192-173
7. Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995, 270: 467-470. DOI: 10.1126/science.270.5235.467
8. Audic S, Claverie JM: The significance of digital gene expression profiles. Genome Res. 1997, 7: 986-995.
9. OMIM. [http://www3.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM]
10. Cardiac gene database. [http://igs-server.cnrs-mrs.fr/Card_Gene/]
11. Tsunoda T, Takagi T: Estimating transcription factor bindability on DNA. Bioinformatics. 1999, 15: 622-630. 10.1093/bioinformatics/15.7.622. DOI: 10.1093/bioinformatics/15.7.622
12. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F: TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res. 2000, 28: 316-319. 10.1093/nar/28.1.316. DOI: 10.1093/nar/28.1.316
13. van Helden J, Andre B, Collado-Vides J: Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol. 1998, 281: 827-842. 10.1006/jmbi.1998.1947. DOI: 10.1006/jmbi.1998.1947
14. Romualdi C, Bortoluzzi S, Danieli GA: Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests. Hum Mol Genet. 2001, 10: 2133-2141. 10.1093/hmg/10.19.2133. DOI: 10.1093/hmg/10.19.2133
15. Bortoluzzi S, d'Alessi F, Danieli GA: A computational reconstruction of the adult human heart transcriptional profile. JMol Cell Cardiol. 2000, 32: 1931-1938. 10.1006/jmcc.2000.1227. DOI: 10.1006/jmcc.2000.1227
16. Hwang DM, Dempsey AA, Lee CY, Liew CC: Identification of differentially expressed genes in cardiac hypertrophy by analysis of expressed sequence tags. Genomics. 2000, 66: 1-14. 10.1006/geno.2000.6171. DOI: 10.1006/geno.2000.6171
17. Schmitt AO, Specht T, Beckmann G, Dahl E, Pilarsky CP, Hinzmann B, Rosenthal A: Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues. Nucleic Acids Res. 1999, 27: 4251-4260. 10.1093/nar/27.21.4251. DOI: 10.1093/nar/27.21.4251
18. Stekel DJ, Git Y, Falciani F: The comparison of gene expression from multiple cDNA libraries. Genome Res. 2000, 10: 2055-2061. 10.1101/gr.GR-1325RR. DOI: 10.1101/gr.GR-1325RR
19. Bortoluzzi S, d'Alessi F, Romualdi C, Danieli GA: The human adult skeletal muscle transcriptional profile reconstructed by a novel computational approach. Genome Res. 2000, 10: 344-349. 10.1101/gr.10.3.344. DOI: 10.1101/gr.10.3.344
20. Liew CC, Hwang DM, Fung YW, Laurenssen C, Cukerman E, Tsui S, Lee CY: A catalogue of genes in the cardiovascular system as identified by expressed sequence tags. Proc Natl Acad Sci USA. 1994, 91: 10645-10649. DOI: 10.1073/pnas.91.22.10645
21. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, et al: Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA. 2002, 99: 4465-4470. 10.1073/pnas.012025199. DOI: 10.1073/pnas.012025199
22. Aydin S, Yilmaz Y, Odabas O, Sekeroglu R, Tarakcioglu M, Atilla MK: A further study of seminal plasma: lactate dehydrogenase and lactate dehydrogenase-X activities and diluted semen absorbance. Eur J Clin Chem Clin Biochem. 1997, 35: 261-264.
23. Fessele S, Maier H, Zischek C, Nelson PJ, Werner T: Regulatory context is a crucial part of gene function. Trends Genet. 2002, 18: 60-63. 10.1016/S0168-9525(02)02591-X. DOI: 10.1016/S0168-9525(02)02591-X
24. Boguski MS, Lowe TM, Tolstoshev CM: dbEST - database for "expressed sequence tags". Nat Genet. 1993, 4: 332-333. DOI: 10.1038/ng0893-332
25. Jurka J: Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000, 16: 418-420. 10.1016/S0168-9525(00)02093-X. DOI: 10.1016/S0168-9525(00)02093-X
26. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. 10.1006/jmbi.1990.9999. DOI: 10.1016/S0022-2836(05)80360-2
27. Huang X: A contig assembly program based on sensitive detection of fragment overlaps. Genomics. 1992, 14: 18-25. DOI: 10.1016/S0888-7543(05)80277-0
28. Sokal R, Michener C: A statistical method for evaluating systematic relationship. Univ Kansas Sci Bull. 1958, 28: 1409-1438.
29. Kuhner MK, Felsenstein J: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates [erratum: Mol Biol Evol 1995 May;12(3):525]. Mol Biol Evol. 1994, 11: 459-468.
30. Entrez Genome. [http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search]
31. Tfbind. [http://tfbind.ims.u-tokyo.ac.jp/]
32. TRANSFAC - the transcription factor database. [http://transfac.mirror.edu.cn/TRANSFAC/]
33. Regulatory sequence analysis tools. [http://rsat.ulb.ac.be/rsat/]
34. Praz V, Perier R, Bonnard C, Bucher P: The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res. 2002, 30: 322-324. 10.1093/nar/30.1.322. DOI: 10.1093/nar/30.1.322
35. Eukaryotic promoter database. [http://www.epd.isb-sib.ch/]
36. Bailey TL, Gribskov M: Methods and statistics for combining motif match scores. J Comput Biol. 1998, 5: 211-221. DOI: 10.1089/cmb.1998.5.211
37. MEME. [http://meme.sdsc.edu/meme/website]