CleanEx: New data extraction and merging tools based on MeSH term annotation

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Praz, Viviane ^a   Bucher, Philipp ^a  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA;

ACCESS TO INFORMATION; ARTICLE; BIOMEDICINE; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA EXTRACTION; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DATABASE; INFORMATION RETRIEVAL; INTERNET; MEDLINE; MESH HEADING; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ANALYSIS; SERIAL ANALYSIS OF GENE EXPRESSION;

ANIMALS; CHROMOSOME MAPPING; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; MEDICAL SUBJECT HEADINGS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 58149199565     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn878     Document Type: Article

References (13)

1. Barrett,T., Troup,D.B., Wilhite,S.E., Ledoux,P., Rudnev,D., Evangelista,C., Kim,I.F., Soboleva,A., Tomashevsky,M., Edgar,R. et al. (2006) NCBI GEO: Mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res., 35, D760-D765.
2. Parkinson et al. (2007) ArrayExpress - a public database of microarray experiments and gene expression profiles. Nucleic Acids Res., 35, D747-D750.
3. Praz,V., Jagannathan,V. and Bucher,P. (2005) CleanEx: A database of heterogeneous gene expression data based on a consistent gene nomenclature. Nucleic Acids Res., 32, D542-D547.
4. Velculescu,V.E., Zhang,L., Vogelstein,B. and Kinzler,K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
5. Brenner,S., Johnson,M., Bridgham,J., Golda,G., Lloyd,D.H., Johnson,D., Luo,S., McCurdy,S., Foy,M., Ewan,M. et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol., 18, 630-634.
6. Rambaldi,D., Felice,B., Prav,V., Bucher,P., Cittaro,D. and Gufanti,A. (2007) Splicy: A web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. BMC Bioinformatics, 8, S17.
7. Ambrosini,G., Praz,V., Jagannathan,V. and Bucher,P. (2003) Signal search analysis server. Nucleic Acids Res., 31, 3618-3620.
8. Malone,J., Rayner,T.F., Bradley,X.Z. and Parkinson,H. (2008) Developing an application focused experimental factor ontology: Embracing the OBO Community. In Proceedings of ISMB 2008 SIG meeting on Bio-ontologies.
9. Rubin,D.L., Shah,N.H. and Noy,N.F. (2008) Biomedical ontologies: A functional perspective. Brief. Bioinform., 9, 75-90.
10. Sperisen,P., Iseli,C., Pagni,M., Stevenson,B.J., Bucher,P. and Jongeneel,C.V. (2004) trome, trEST and trGEN: Databases of predicted protein sequences. Nucleic Acids Res., 32, D509-D511.
11. Iseli,C., Ambrosini,G., Bucher,P. and Jongeneel,C.V. (2007) Indexing strategies for rapid searches of short words in genome sequences. PLoS One, 2, e579.
12. Herrero,J., Al-Shahrour,F., Díaz-Uriarte,R., Mateos,Á., Vaquerizas,J.M., Santoyo,J. and Dopazo,J. (2003) GEPAS, a web-based resource for microarray gene expression data analysis. Nucleic Acids Res., 31, 3461-3467.
13. Bailey,T.L., Williams,N., Misleh,C. and Li,W.W. (2006) MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res., 34, W369-W373.