Differentially expressed genes

GP Yang, DT Ross, WW Kuang, PO Brown, RJ Weigel. Combining SSH and cDNA microar-rays for rapid identification of differentially expressed genes. Nucleic Acids Res 27 1517-1523, 1999. 

Differential display is a method for identifying differentially expressed genes, using anchored oligo-dT, random oligonucleotide primers and polymerase chain reaction on reverse-transcribed RNA from different cell populations. The amplified complementary DNAs are displayed and comparisons are drawn between the different cell populations. 

Chen, M.-L. Chen, C.-H. (2005b). Microarray analysis of differentially expressed genes in rat frontal cortex under chronic risperidone treatment. Neuropsychopharmacology, 30(2), 268-77. 

Gottschlich S et al 1. Differentially expressed genes in head and neck cancer. Laryngoscope 1998 108 639-644. 

Oh S-W et al. Identification of differentially expressed genes in human hepatoblastoma cell line (HepG2] and HBV-X transfected hepatobalstoma cell line (HepG2-4X). Col Cells 1998 8 212-218. 

Quantitative RT PCR (qRT PCR) can be used to accurately determine the levels of messages within given preparations of RNA. qRT PCR thermocyclers provide rapid online detection and quantification of mRNA, however, the initial purchase cost and the cost of reagents may be prohibitive for some laboratories. Methods of semiquantitative RT PCR have been used and good descriptions of these techniques are available (Samhrook and Russell, 2001). However, the same cDNA populations should not be used for differential display reactions and verification that a potential differential display band represents a differentially expressed gene. For this reason, independent cDNA samples should be prepared if both the screening and verification methods rely on PCR. qRT PCR, therefore, should be used in conjunction with other methods to verify that a differential display band represents a differentially expressed gene. 

Jurecic R, Nachtman RG, Colicos SM, Belmont JW. 1998. Identification and cloning of differentially expressed genes by long-distance differential display. Anal Biochem 259 235. 

Dudoit S, Yang YH, Callow MJ, Speed TP. 2002. Statistical methods for identifying differentially expressed genes in replicate cDNA microarray experiments. Statistica Sinica 12 111. 

Pan W. 2002. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 18 546. 

Figure 2.8 Microarray cross-platform showing differentially expressed gene clusters obtained from Amersham, Agilent, and Affymetrix products. (From Barczak, A., etal., Genome Res., 13, 1775-1785, 2003 [Copyright 2003 Cold Spring Harbor Laboratory Press] and Tan, P.K. etal.. Nucleic Acid Res., 31(19), 5676-5684, 2003. With permission.)...

Of the 4224 cDNA clones, a total of 159 (82 nonredxmdant genes) were observed to be differentially expressed over the 14-day period. Most genes were found to be up-regulated by day 5 and very few genes down-regulated. The differentially expressed genes were divided into four clusters for the purpose of analysis ... 

While only -10% of microarray datasets address the problem of batch effects (48), the degree of error contributed by batch effects may be significant. Batch effects may include experimental variations introduced due to multiple types of technical bias (e.g., time, laboratory, reagents, handling). Analysis of multiple methods to address batch effects has been addressed for precision, accuracy, and overall performance (48). Once probe set raw intensities have been processed via normalization and possible additional corrective measures, values can be used for downstream analyses in identifying differentially expressed genes and corresponding functional associations. 

Zom KK, Jazaeri AA, Awtrey CS et al. Choice of normal ovarian control influences determination of differentially expressed genes in ovarian cancer expression profiling studies. Clin Cancer Res 2003 9 4811 818. 

Simon et al. (14) also showed that cross-validating the prediction rule after selection of differentially expressed genes from the full data set does little to correct the bias of the re-substitution estimator 90.2% of simulated data sets with no true relationship between expression data and class still result in zero misclassifications. When feature selection was also re-done in each cross-validated training set, however, appropriate estimates of mis-classification error were obtained the median estimated misclassification rate was approximately 50%. 

Moreover gene-expression analysis of leukemia cells from B-lineage acute lymphoblastic leukemia pediatric patients has identified sets of differentially expressed genes that are associated specifically with sensitivity or resistance to chemotherapy. Such information can also be used in diagnostic assay to stratify the patients in sub-categories, to develop new drugs and later on to personalize the anti-cancer therapy. 

Shim, C., Zhang, W., Ree, C. H., and Lee, J.-H. 1998. Profiling of differentially expressed genes in human primary cervical cancer by complementary DNA expression array. Clin. Cancer Res. 4 3045-3050. 

Underwood LJ, Tanimoto H, Wang Y, Shigemasa K, Parmley TH, O Brien TJ. Cloning of tumor-associated differentially expressed gene-14, a novel serine protease overexpressed by ovarian carcinoma. Cancer Res 1999 59 4435 1439. 

Kaestner K. H., Ntambi J. M., Kelly T. J. and Lane, M. D. (1989) Differentiation-induced gene expression in 3T3-L1 preadipocytes - a second differentially expressed gene encoding stearoyl-CoA desaturase. J. Biol. Chem. 264, 14755-14761. 

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