About Our Array Analysis Solutions
The aim has always been to allow researchers to mine their Affymetrix data with the same intuitive logic of a 'literature search‘. In other words, creating and comparing sets of genes to enable rapid movement onto the next phase of any microarray expeirment… the FOLLOW UP of interesting results!
Features which have really stuck a chord with the bench scientist are:
- the power to easily distinguish genuine fold-changes from baseline noise
- the abilty for researchers to work on their own data on their own machines in their own time without having to rely on high-end and expensive computing tools or bionformaticians
Indeed, using our tools, many groups have found that they are able to move to the next phase of their biological experiments (and thus to publication) much more rapidly than they anticipated. A list of papers that have used this approach are below.
Our solutions are based on the tried and tested microarray analysis tools designed by A/Prof Gareth Denyer at the University of Sydney, Australia.
from the University of Applied Science, Weihenstephan, Germany, and working under the guidance of Professor Denyer, has reworked the tools so that they run on the fast and robust platforms of Java and MySQL.
Peter and Gareth are keen for other developers to leverage off what they have created and would certainly entertain requests to make their code and insights available to other bioinformaticians.
Publications that have used our analysis tool logic include:
- Bunting K, Rao S, Hardy K, Woltring D, Denyer GS, Wang J, Gerondakis S, Shannon MF. Genome-wide analysis of gene expression in T cells to identify targets of the NF-kappa B transcription factor c-Rel. J Immunol. 2007 Jun 1;178(11):7097-109. PMID: 17513759
- Nguyen LL, Kriketos AD, Hancock DP, Caterson ID, Denyer GS. Insulin resistance does not influence gene expression in skeletal muscle. J Biochem Mol Biol. 2006 Jul 31;39(4):457-63. PMID: 16889692
- Busch AK, Gurisik E, Cordery DV, Sudlow M, Denyer GS, Laybutt DR, Hughes WE, Biden TJ. Increased fatty acid desaturation and enhanced expression of stearoyl coenzyme A desaturase protects pancreatic beta-cells from lipoapoptosis. Diabetes. 2005 Oct;54(10):2917-24. PMID: 16186393
- Singh J, Manickam P, Shmoish M, Natik S, Denyer G, Handelsman D, Gong DW, Dong Q. Annotation of androgen dependence to human prostate cancer-associated genes by microarray analysis of mouse prostate. Cancer Lett. 2006 Jun 18;237(2):298-304. Epub 2005 Jul 15. PMID: 16024171
- Lal S, Lui R, Nguyen L, Macdonald P, Denyer G, dos Remedios C. Increases in leukocyte cluster of differentiation antigen expression during cardiopulmonary bypass in patients undergoing heart transplantation. Proteomics. 2004 Jul;4(7):1918-26. Erratum in: Proteomics. 2004 Nov;4(11):3660. PMID: 15221749
- McElwaine S, Mulligan C, Groet J, Spinelli M, Rinaldi A, Denyer G, Mensah A, Cavani S, Baldo C, Dagna-Bricarelli F, Hann I, Basso G, Cotter FE, Nizetic D. Microarray transcript profiling distinguishes the transient from the acute type of megakaryoblastic leukaemia (M7) in Down's syndrome, revealing PRAME as a specific discriminating marker. Br J Haematol. 2004 Jun;125(6):729-42. PMID: 15180862
- Johnson NA, Sengupta S, Saidi SA, Lessan K, Charnock-Jones SD, Scott L, Stephens R, Freeman TC, Tom BD, Harris M, Denyer G, Sundaram M, Sasisekharan R, Smith SK, Print CG. Endothelial cells preparing to die by apoptosis initiate a program of transcriptome and glycome regulation. FASEB J. 2004 Jan;18(1):188-90. Epub 2003 Nov 20. PMID: 14630703
- Mulligan C, Rochford J, Denyer G, Stephens R, Yeo G, Freeman T, Siddle K, O'Rahilly S. Microarray analysis of insulin and insulin-like growth factor-1 (IGF-1) receptor signaling reveals the selective up-regulation of the mitogen heparin-binding EGF-like growth factor by IGF-1. J Biol Chem. 2002 Nov 8;277(45):42480-7. Epub 2002 Sep 3. PMID: 12213819
- Busch AK, Cordery D, Denyer GS, Biden TJ. Expression profiling of palmitate- and oleate-regulated genes provides novel insights into the effects of chronic lipid exposure on pancreatic beta-cell function. Diabetes. 2002 Apr;51(4):977-87. PMID: 11916915