GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages 221-

  Risueño, Alberto ^a   Fontanillo, Celia ^a   Dinger, Marcel E ^b   De Las Rivas, Javier ^a  

^a CSIC   (Spain)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AFFYMETRIX GENECHIP; AFFYMETRIX MICROARRAYS; BIOLOGICAL SAMPLES; EXPRESSION MICROARRAY; INTEGRATED DATABASE; INTERACTIVE EXPLORATION; MICROARRAY EXPERIMENTS; MICROARRAY TECHNOLOGIES;

DATABASE SYSTEMS; MAPPING; MICROARRAYS; NUCLEOTIDES; PROBES; PROTEINS; VISUALIZATION;

GENE EXPRESSION;

METAZOA; RATTUS;

UNTRANSLATED RNA;

ANIMAL; ARTICLE; CHEMISTRY; CHROMOSOME MAP; COMPUTER PROGRAM; DNA MICROARRAY; EXON; GENE EXPRESSION PROFILING; GENE LOCUS; GENETIC DATABASE; GENETICS; GENOME; GENOMICS; HUMAN; METHODOLOGY; MOUSE; OLIGONUCLEOTIDE PROBE; RAT;

ANIMALS; CHROMOSOME MAPPING; DATABASES, GENETIC; EXONS; GENE EXPRESSION PROFILING; GENETIC LOCI; GENOME; GENOMICS; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; RATS; RNA, UNTRANSLATED; SOFTWARE;

EID: 77951531009     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-221     Document Type: Article

References (31)

1. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1663. 10.1126/science.1112014, 16141072.
2. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316:1484-1488. 10.1126/science.1138341, 17510325.
3. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, et al. Ensembl 2009. Nucleic Acids Res 2009, 37:D690-D697. 10.1093/nar/gkn828, 2686571, 19033362.
4. Pang KC, Stephen S, Dinger ME, Engström PG, Lenhard B, Mattick JS. RNAdb 2.0: an expanded database of mammalian non-coding RNAs. Nucleic Acids Res 2007, 35:D178-D182. 10.1093/nar/gkl926, 1751534, 17145715.
5. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, 37:D885-D890. 10.1093/nar/gkn764, 2686538, 18940857.
6. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101:6062-6067. 10.1073/pnas.0400782101, 395923, 15075390.
7. Gellert P, Uchida S, Braun T. Exon Array Analyzer: a web interface for Affymetrix exon array analysis. Bioinformatics 2009, 25:3323-3324. 10.1093/bioinformatics/btp577, 19808879.
8. Muro EM, Herrington R, Janmohamed S, Frelin C, Andrade-Navarro MA, Iscove NN. Identification of gene 3' ends by automated EST cluster analysis. Proc Natl Acad Sci USA 2008, 105:20286-20290. 10.1073/pnas.0807813105, 2629301, 19095794.
9. Sandberg R, Larsson O. Improved precision and accuracy for microarrays using updated probe set definitions. BMC Bioinformatics 2007, 8:48. 10.1186/1471-2105-8-48, 1805763, 17288599.
10. Liu WM, Mei R, Di X, Ryder TB, Hubbell E, Dee S, Webster TA, Harrington CA, Ho MH, Baid J, Smeekens SP. Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 2002, 18:1593-1599. 10.1093/bioinformatics/18.12.1593, 12490443.
11. Hochreiter S, Clevert DA, Obermayer K. A new summarization method for Affymetrix probe level data. Bioinformatics 2006, 22(8):943-949. 10.1093/bioinformatics/btl033, 16473874.
12. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31(4):e15. 10.1093/nar/gng015, 150247, 12582260.
13. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
14. Barash Y, Dehan E, Krupsky M, Franklin W, Geraci M, Friedman N, Kaminski N. Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics 2004, 20:839-846. 10.1093/bioinformatics/btg487, 14751998.
15. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121. 10.1073/pnas.091062498, 33173, 11309499.
16. Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, et al. Genome Information Integration Project And H-Invitational 2 The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 2008, 36:D793-799. 10.1093/nar/gkm999, 2238988, 18089548, Genome Information Integration Project And H-Invitational 2.
17. Mercer TR, Dinger ME, Mattick JS. Long noncoding RNAs: insights into functions. Nat Rev Genet 2009, 10:155-159. 10.1038/nrg2521, 19188922.
18. Dinger ME, Amaral PP, Mercer TR, Mattick JS. Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Brief Funct Genomic Proteomic 2009, 8:407-423. 10.1093/bfgp/elp038, 19770204.
19. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
20. Brent MR. Genome annotation past, present, and future: How to define an ORF at each locus. Genome Res 2005, 15:1777-1786. 10.1101/gr.3866105, 16339376.
21. Mattick JS, Taft RJ, Faulkner GJ. A global view of genomic information - moving beyond the gene and the master regulator. Trends Genet 2009, 26:21-28. 10.1016/j.tig.2009.11.002, 19944475.
22. Gautier L, Møller M, Friis-Hansen L, Knudsen S. Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics 2004, 5:111. 10.1186/1471-2105-5-111, 514699, 15310390.
23. Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 2005, 33:e175. 10.1093/nar/gni179, 1283542, 16284200.
24. Harbig J, Sprinkle R, Enkemann SA. A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array. Nucleic Acids Res 2005, 33:e31. 10.1093/nar/gni027, 549426, 15722477.
25. Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z. Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 2005, 6:107. 10.1186/1471-2105-6-107, 1127107, 15850491.
26. Leong HS, Yates T, Wilson C, Miller CJ. ADAPT: a database of affymetrix probesets and transcripts. Bioinformatics 2005, 21:2552-2553. 10.1093/bioinformatics/bti359, 15746287.
27. Lu J, Lee JC, Salit ML, Cam MC. Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays. BMC Bioinformatics 2007, 8:108. 10.1186/1471-2105-8-108, 1853115, 17394657.
28. Liu H, Zeeberg BR, Qu G, Koru AG, Ferrucci A, Kahn A, Ryan MC, Nuhanovic A, Munson PJ, Reinhold WC, Kane DW, Weinstein JN. AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics 2007, 23:2385-2390. 10.1093/bioinformatics/btm360, 17660211.
29. Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S. Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics 2007, 8:446. 10.1186/1471-2105-8-446, 2216044, 18005434.
30. Yates T, Okoniewski MJ, Miller CJ. X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis. Nucleic Acids Res 2008, 36:D780-786. 10.1093/nar/gkm779, 2238884, 17932061.
31. Gellert P, Uchida S, Braun T. Exon Array Analyzer: a web interface for Affymetrix exon array analysis. Bioinformatics 2009, 25:3323-3324. 10.1093/bioinformatics/btp577, 19808879.