Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Keime, Céline ^a   Damiola, Francesca ^a   Mouchiroud, Dominique ^a   Duret, Laurent ^a   Gandrillon, Olivier ^a  

^a UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CELL POPULATIONS; FUNCTIONAL ANNOTATION; GENE EXPRESSION ANALYSIS; IDENTIFICATION PARAMETERS; INTERCONNECTED MODULES; RELATIONAL DATABASE; SERIAL ANALYSIS OF GENE EXPRESSIONS; TAG IDENTIFICATION;

ANIMALS; CELL CULTURE; CELL PROLIFERATION; DATABASE SYSTEMS; GENE EXPRESSION; TOOLS; WEBSITES;

LIBRARIES;

COMPLEMENTARY DNA; MESSENGER RNA; TRANSCRIPTOME; POLYADENYLIC ACID;

ACCESS TO INFORMATION; ACCURACY; ARTICLE; CELL POPULATION; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; FREQUENCY ANALYSIS; GENE IDENTIFICATION; GENE LIBRARY; GENE MAPPING; GENETIC TRANSCRIPTION; HUMAN; INFORMATION PROCESSING; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE DATABASE; SERIAL ANALYSIS OF GENE EXPRESSION; SPECIES DIFFERENCE; TIME; ANIMAL; CHICKEN; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; PROCEDURES; SEQUENCE HOMOLOGY;

GALLUS GALLUS; SALVIA;

ANIMALS; CHICKENS; DATABASES, GENETIC; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; HUMANS; POLY A; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; SOFTWARE DESIGN; SPECIES SPECIFICITY;

EID: 13244277569     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-143     Document Type: Article

References (20)

1. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW: Serial analysis of gene expression. Science 1995, 270:484-487.
2. SAGEmap [http://www.ncbi.nlm.nih.gov/SAGE/index.cgi]
3. SAGE Genie [http://cgap.nci.nih.gov/SAGE]
4. Melbourne Brain Genome Project [http://www.mbgproject.org/]
5. Mouse SAGE site [http://mouse.biomed.cas.cz/sage/]
6. Human Transcriptome Map [http://bioinfo.amc.uva.nl/HTMseq/controller]
7. SAGEnet [http://www.sagenet.org/index.htm]
8. Boardman PE, Sanz-Ezquerro J, Overton IM, Burt DW, Bosch E, Fong WT, Tickle C, Brown WR, Wilson SA, Hubbard SJ: A Comprehensive Collection of Chicken cDNAs. Curr Biol 2002, 12:1965-1969.
9. MySQL [http://www.mysql.com/]
10. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 389-3402.
11. Perriere G, Gouy M: WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 1996, 78:364-369.
12. Gandrillon O, Schmidt U, Beug H, Samarut J: TGFβ cooperates with TGFα to induce the self-renewal of normal erythrocytic progenitors: Evidence for an autocrine mechanism. EMBO J 1999, 18:2764-2781.
13. Damiola F, Keime C, Gonin-Giraud S, Dazy S, Gandrillon O: Global transcription analysis of immature avian erythrocytic progenitors : from self-renewal to differentiation. Oncogene 2004, 23 7628-7643.
14. SAGE2000 [http://www.sagenet.org/Software/software2000.htm]
15. Blastclust [ftp://ftp.ncbi.nih.gov/blast/executables/LATEST]
16. Piquemal D, Commes T, Manchon L, Lejeune M, Ferraz C, Pugnere D, Demaille J, Elalouf J, Marti J: Transcriptome analysis of monocytic leukemia cell differentiation. Genomics 2002, 80:361-371.
17. Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE: Using the transcriptome to annotate the genome. Nat Biotechnol 2002, 20:508-512.
18. Fitch WM: Distinguishing homologous from analogous proteins. Syst Zool 1970, 19:99-113.
19. Yanai I, Graur D, Ophir R: Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. Omics 2004, 8:15-24.
20. Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, Muetzel B, Wirkner U, Ansorge W, Paabo S: A neutral model of transcriptome evolution. PLoS Biol 2004, 2:E132.