Gene expression measurements

MAQC Consortium (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24(9) 1151-1161... 

Friedman et al. (2000) tested this approach on a data set for yeast cell cycle expression patterns provided by Spellman and co-workers (1998), writing that This data set contains 76 gene expression measurements of the mRNA levels of 6177 S. cerevisiae ORFs. These experiments measure six... 

Biomolecular MS and in particular MALDI-TOF-MS (see Sections 2.1.22 and 2.2.1) permit the routine analysis of oligonucleotides up to 70-mers, intact nucleic acids, and the direct detection of DNA products with no primer labels with an increase in analysis speed and mass accuracy especially in contrast to traditional DNA separation techniques such as slab gels or capillary electrophoresis. Applications focus on the characterization of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Precise and accurate gene expression measurements show relative and absolute numbers of target molecules determined independently of the number of PCR cycles. DNA methylation can be studied quantitatively. 

Gilbert RW, Costain WJ, Blanchard ME, Mullen K, Currie RW, et al. 2003. DNA microarray analysis of hippocampal gene expression measured 12 hours after hypoxia-ischemia in the mouse. J Cereb Blood Flow Metabol 23 1195. 

Another important issue is what can be used to predict change in protein levels. In a review of the literature, it is apparent from the measurements in yeast and mouse liver that there is yet no strong correlation between mRNA level and that of proteins, especially in the case of poorly expressed genes. Therefore, conducting gene expression measurements may not be sufficient to infer protein expression. Thus, the analytical methods used in proteomics must provide detection of proteomes present in multiple-modified forms at relatively low levels. 

Fig. 15 Internalization and gene expression of pDNA released from a multilayer assembly. Release of pDNA occurs upon degradation of T4 polyamide. Notable increase in fluorescence intensity overtime is observed in the flow histograms. Gene expression (measured by intracellular GFP fluorescence) does not increase at the same rate as DNA uptake. Figure adapted with permission from [151]. 2009 Elsevier...

M. C. Evaluation of gene expression measurements from commercial microarray platforms. Nucl. Acids. Res. 2003, 31, 5676-5684. 

Ronald, J., Akey, J.M., Whittle, J., Smith, E.N., Yvert, G., and Kruglyak, L. 2005. Simultaneous genotyping, gene expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Gen. Res. 15,284-291. 

D. Z. Wetmore, T.J. Mariani, I.S. Kohane, Z. Szallasi, Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements, Nucleic Acids Res. 2004, 32, e74. 

N. P. Gerry, M.E. Lenburg, C.L. Rosenberg, Reliability and reproducibility of gene expression measurements using amplified RNA from laser-microdissected primary breast tissue with oligonucleotide arrays, J. Mol. Diagn. 2005, 7, 57-64. 

Purified CrylAc (formerly CrylA(c)) toxin (lepidopteran-active) fed at a concentration of 20 Jig/ml to 1-3-day-old larvae and adults of Apis mellif-era had no significant effect on the survival of these insects [44]. This toxin concentration was more than 100 times the concentration of CrylAc protein found in the field as present in pollen and nectar of transgenic cotton [44], but the authors did not give details of these gene expression measurements. Similarly, purified Cry3Ba (formerly CrylllB) toxin (coleopteran-active) fed in sugar syrup at concentrations of 0.066 or 0.332... 

Matsunaga, H., Anazawa, T., and Yeung, E.S., Integrated on-capUlary instrumentation for gene expression measurement directly from cells. Electrophoresis, 24, 458, 2003. 

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