AnnotQTL: A new tool to gather functional and comparative information on a genomic region

Nucleic Acids Research

Volumn 39, Issue SUPPL. 2, 2011, Pages

  Lecerf, F ^a,b   Bretaudeau, A ^c   Sallou, O ^c   Desert, C ^a,b   Blum, Y ^a,b   Lagarrigue, S ^a,b   Demeure, O ^a,b  

^a CEMAGREF   (France)

^b AGROCAMPUS OUEST   (France)

^c CAMPUS DE BEAULIEU   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MYOSTATIN;

ARTICLE; COMPARATIVE GENE MAPPING; COMPUTER PROGRAM; CONTROLLED STUDY; GENE IDENTIFICATION; GENE LOCATION; GENE MUTATION; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC DATABASE; GENOMICS; HUMAN; INFORMATION PROCESSING; INTERNET; MUSCLE HYPERTROPHY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES COMPARISON;

ANIMALS; CATTLE; GENOMICS; HUMANS; INTERNET; LIVESTOCK; MICE; MOLECULAR SEQUENCE ANNOTATION; QUANTITATIVE TRAIT LOCI; SOFTWARE;

MAMMALIA;

EID: 79960026127     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr361     Document Type: Article

References (21)

1. Yue, P., Melamud, E. and Moult, J. (2006) SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics, 7, 166-166.
2. Goodswen, S., Gondro, C., Watson-Haigh, N. and Kadarmideen, H. (2010) FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. BMC Bioinformatics, 11, 311.
3. Wang, P., Dai, M., Xuan, W., McEachin, R.C., Jackson, A.U., Scott, L.J., Athey, B., Watson, S.J. and Meng, F. (2006) SNP Function Portal: a web database for exploring the function implication of SNP alleles. Bioinformatics, 22, e523-e529. (Pubitemid 44288324)
4. Shen, T.H., Carlson, C.S. and Tarczy-Hornoch, P. (2009) SNPit: a federated data integration system for the purpose of functional SNP annotation. Comp. Methods Prog. Biomedicine, 95, 181-189.
5. Ryan, M., Diekhans, M., Lien, S., Liu, Y. and Karchin, R. (2009) LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics, 25, 1431-1432.
6. Riva, A. and Kohane, I.S. (2004) A SNP-centric database for the investigation of the human genome. BMC Bioinformatics, 5, 33.
7. Reumers, J., Maurer-Stroh, S., Schymkowitz, J. and Rousseau, F. (2006) SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics, 22, 2183-2185. (Pubitemid 44390919)
8. Li, S., Ma, L., Li, H., Vang, S., Hu, Y., Bolund, L. and Wang, J. (2007) Snap: an integrated SNP annotation platform. Nucleic Acids Res., 35, D707-D710. (Pubitemid 46056296)
9. Haider, S., Ballester, B., Smedley, D., Zhang, J., Rice, P. and Kasprzyk, A. (2009) BioMart Central Portal-unified access to biological data. Nucleic Acids Res., 37, W23-W27.
10. Courcelle, E., Beausse, Y., Letort, S., Stahl, O., Fremez, R., Ngom- Bru, C., Gouzy, J. and Faraut, T. (2008) Narcisse: a mirror view of conserved syntenies. Nucleic Acids Res., 36, D485-D490. (Pubitemid 351149771)
11. Filangi, O., Beausse, Y., Assi, A., Legrand, L., Larre, J.M., Martin, V., Collin, O., Caron, C., Leroy, H. and Allouche, D. (2008) BioMAJ: a flexible framework for databanks synchronization and processing. Bioinformatics, 24, 1823-1825.
12. Charlier, C., Coppieters, W., Farnir, F., Grobet, L., Leroy, P.L., Michaux, C., Mni, M., Schwers, A., Vanmanshoven, P., Hanset, R. et al. (1995) The mh gene causing double-muscling in cattle maps to bovine Chromosome 2. Mamm. Genome, 6, 788-792.
13. Grobet, L., Martin, L.J., Poncelet, D., Pirottin, D., Brouwers, B., Riquet, J., Schoeberlein, A., Dunner, S., Menissier, F., Massabanda, J. et al. (1997) A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nat. Genet., 17, 71-74. (Pubitemid 27377534)
14. Lagarrigue, S., Pitel, F., Carre, W., Abasht, B., Le Roy, P., Neau, A., Amigues, Y., Sourdioux, M., Simon, J., Cogburn, L. et al. (2006) Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness. Genet. Sel. Evol., 38, 85-97. (Pubitemid 43075125)
15. Le Mignon, G., Pitel, F., Gilbert, H., Le Bihan-Duval, E., Vignoles, F., Demeure, O., Lagarrigue, S., Simon, J., Cogburn, L.A., Aggrey, S.E. et al. (2009) A comprehensive analysis of QTL for abdominal fat and breast muscle weights on chicken chromosome 5 using a multivariate approach. Anim. Genet., 40, 157-164.
16. Blum, Y., Le Mignon, G., Lagarrigue, S. and Causeur, D. (2010) A factor model to analyze heterogeneity in gene expression. BMC Bioinformatics, 11, 368.
17. Le Mignon, G., Desert, C., Pitel, F., Leroux, S., Demeure, O., Guernec, G., Abasht, B., Douaire, M., Le Roy, P. and Lagarrigue, S. (2009) Using transcriptome profiling to characterize QTL regions on chicken chromosome 5. BMC Genomics, 10, 575.
18. Ponsuksili, S., Jonas, E., Murani, E., Phatsara, C., Srikanchai, T., Walz, C., Schwerin, M., Schellander, K. and Wimmers, K. (2008) Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle. BMC Genomics, 9, 367.
19. Babak, T., Garrett-Engele, P., Armour, C.D., Raymond, C.K., Keller, M.P., Chen, R., Rohl, C.A., Johnson, J.M., Attie, A.D., Fraser, H.B. et al. (2010) Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation. BMC Genomics, 11, 473.
20. Drost, D.R., Benedict, C.I., Berg, A., Novaes, E., Novaes, C.R., Yu, Q., Dervinis, C., Maia, J.M., Yap, J., Miles, B. et al. (2010) Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus. Proc. Natl Acad. Sci. USA, 107, 8492-8497.
21. van Nas, A., Ingram-Drake, L., Sinsheimer, J.S., Wang, S.S., Schadt, E.E., Drake, T. and Lusis, A.J. (2010) Expression quantitative trait loci: replication, tissue- and sex-specificity in mice. Genetics, 185, 1059-1068.