EXP-PAC: Providing comparative analysis and storage of next generation gene expression data

Genomics

Volumn 100, Issue 1, 2012, Pages 8-13

  Church, Philip C ^a   Goscinski, Andrzej ^a   Lefèvre, Christophe ^a  

^a DEAKIN UNIVERSITY   (Australia)

Author keywords

Comparative analysis; Database; Gene expression; Microarray

Indexed keywords

ACCESS TO INFORMATION; ACCURACY; ALGORITHM; ARTICLE; COMPARATIVE STUDY; COMPUTER INTERFACE; CONTROLLED STUDY; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; GENE EXPRESSION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC DATABASE; GENOME ANALYSIS; MICROARRAY ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; SENSITIVITY AND SPECIFICITY; SIGNAL PROCESSING; WEB BROWSER;

GENE EXPRESSION PROFILING; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84862753124     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2012.05.007     Document Type: Article

References (31)

1. Strahm Y., Powell D., Lefevre C. EST-PAC a web package for EST annotation and protein sequence prediction. Source Code Biol. Med. 2006, 1:2.
2. Gentleman R., Carey V., Bates D., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J., Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
3. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:8.
4. Iseli C., Jongeneel C.V., Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. presented at the Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology 1999.
5. Sonnhammer E., Eddy S., Birney E., Bateman A., Durbin R. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. January 1, 1998, 26:320-322.
6. Nam S.-H., Kim D.-W., Jung T.-S., Choi Y.-S., Kim D.-W., Choi H.-S., Choi S.-H., Park H.-S. PESTAS: a web server for EST analysis and sequence mining. Bioinformatics July 15, 2009, 25:1846-1848.
7. Meinel T., Schweiger M., Ludewig A., Chenna R., Krobitsch S., Herwig R. Ortho2ExpressMatrix-a web server that interprets cross-species gene expression data by gene family information. BMC Genomics 2011, 12:483.
8. Rayner T., Rocca-Serra P., Spellman P., Causton H., Farne A., Holloway E., Irizarry R., Liu J., Maier D., Miller M., Petersen K., Quackenbush J., Sherlock G., Stoeckert C., White J., Whetzel P., Wymore F., Parkinson H., Sarkans U., Ball C., Brazma A. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinf. 2006, 7:489.
9. Barrett T., Suzek T.O., Troup D.B., Wilhite S.E., Ngau W.-C., Ledoux P., Rudnev D., Lash A.E., Fujibuchi W., Edgar R. NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Res. January 1, 2005, 33:D562-566.
10. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics April 1, 2003, 4:249-264.
11. Hubbell E., Liu W.-M., Mei R. Robust estimators for expression analysis. Bioinformatics December 1, 2002, 18:1585-1592.
12. Wu Z., Irizarry R., Gentleman R., Martinez-Murillo F., Spencer F. A model-based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc. 2004, 99:909.
13. Affymetrix I. Technical note: guide to probe logarithmic intensity error (PLIER) estimation Available:. http://www.affymetrix.com/support/technical/technotes/plier_technote.pdf.
14. Anderson S., Rudolph M., McManaman J., Neville M. Key stages in mammary gland development. Secretory activation in the mammary gland: it's not just about milk protein synthesis!. Breast Cancer Res. 2007, 9:204.
15. Ron M., Israeli G., Seroussi E., Weller J., Gregg J., Shani M., Medrano J. Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle. BMC Genomics 2007, 8:183.
16. Stein T., Morris J., Davies C., Weber-Hall S., Duffy M.-A., Heath V., Bell A., Ferrier R., Sandilands G., Gusterson B. Involution of the mouse mammary gland is associated with an immune cascade and an acute-phase response, involving LBP, CD14 and STAT3. Breast Cancer Res. 2004, 6:R75-R91.
17. Shu D.P., et al. Global transcriptional profiling in porcine mammary glands from late pregnancy to peak lactation. OMICS 2012, 16:123-137.
18. Lefèvre C.M., Sharp J.A., Nicholas K.R. Evolution of lactation: ancient origin and extreme adaptations of the lactation system. Annu. Rev. Genomics Hum. Genet. 2010, 11:219-238.
19. Niederreither K., Subbarayan V., Dollé P., Chambon P. Embryonic retinoic acid synthesis is essential for early mouse post-implantation development. Nat. Genet. 1999, 21:444-448.
20. Hiss S., Mielenz M., Bruckmaier R.M., Sauerwein H. Haptoglobin concentrations in blood and milk after endotoxin challenge and quantification of mammary Hp mRNA expression. J. Dairy Sci. 2004, 87:3778-3784.
21. Kouros-Mehr H., Werb Z. Candidate regulators of mammary branching morphogenesis identified by genome-wide transcript analysis. Dev. Dyn. 2006, 235:3404-3412.
22. Bremel R.D., Shaw M.E. Actomyosin from mammary myoepithelial cells and phosphorylation by myosin light chain kinase. J. Dairy Sci. 1978, 61:1561-1566.
23. Fraser D. A review of the behavioural mechanism of milk ejection of the domestic pig. Appl. Anim. Ethol. 1980, 6:247-255.
24. Cawley N.X., Zhou J., Hill J.M., Abebe D., Romboz S., Yanik T., Rodriguiz R.M., Wetsel W.C., Loh Y.P. The carboxypeptidase E knockout mouse exhibits endocrinological and behavioral deficits. Endocrinology December 1, 2004, 145:5807-5819.
25. Patterson E.E., Minor K.M., Tchernatynskaia A.V., Taylor S.M., Shelton G.D., Ekenstedt K.J., Mickelson J.R. A canine DNM1 mutation is highly associated with the syndrome of exercise-induced collapse. Nat. Genet. 2008, 40:1235-1239.
26. Williams C., Helguero L., Edvardsson K., Haldosen L.-A., Gustafsson J.-A. Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression. Breast Cancer Res. 2009, 11:R26.
27. Wenz H.M., Hinck L., Cannon P., Navre M., Ringold G.M. Reduced expression of AP27 protein, the product of a growth factor-repressible gene, is associated with diminished adipocyte differentiation. Proc. Natl. Acad. Sci. February 1, 1992, 89:1065-1069.
28. Kim S.W., Hurley W.L., Han I.K., Easter R.A. Changes in tissue composition associated with mammary gland growth during lactation in sows. J. Anim. Sci. September 1, 1999, 77:2510-2516.
29. Munford R.E. Changes in the mammary glands of rats and mice during pregnancy, lactation and involution. J. Endocrinol. December 1, 1963, 28:17-34.
30. Kim S.W., Osaka I., Hurley W.L., Easter R.A. Mammary gland growth as influenced by litter size in lactating sows: impact on lysine requirement. J. Anim. Sci. December 1, 1999, 77:3316-3321.
31. Gentzsch W. Sun grid engine: towards creating a compute power grid. presented at the Proceedings of the 1st International Symposium on Cluster Computing and the Grid 2001.