Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions

Genome-scale microarray experiments for comparative analysis of gene expressions produce massive amounts of information. Traditional statistical approaches fail to achieve the required accuracy in sensitivity and specificity of the analysis. Since the problem can be resolved neither by increasing the number of replicates nor by manipulating thresholds, one needs a novel approach to the analysis. This article describes methods to improve the power of microarray analyses by defining internal standards to characterize features of the biological system being studied and the technological processes underlying the microarray experiments. Applying these methods, internal standards are identified and then the obtained parameters are used to define (i) genes that are distinct in their expression from background; (ii) genes that are differentially expressed; and finally (iii) genes that have similar dynamical behavio

Protein Expression During Murine Thymus Differentiation

Driven by our long-standing interest in identifying proteins of the immune system and in characterizing processes involved in lymphocyte differentiation, we studied protein expression in biosynthetically labeled fetal and newborn thymus by 2D gel electrophoresis. Autoradiographs of the gels were scanned with a densitometer and image analysis was performed using the Kepler system. Calibrated polypeptide spot abundances (volumes) were compared to assesses qualitative and quantitative changes of the spot volumes. Among over 300 proteins evaluated at GD (gestation day) 13,15, and 17, there were sets of proteins that increased and others that decreased in intensity. We could in addition recognize proteins that were completely absent at GD 13 and/or 15 and that appeared thereafter to gradually increase in intensity. Conversely, various polypeptide spots present at early stages (at GD 13 and 15) disappear later (at GD 17 or at birth). Among the proteins that increase in intensity prevail molecules with masses less than 35 kD, whereas a considerable portion of those that decrease in intensity are characterized by masses above 60 kD. Spots reported in this communication were not defined beyond tagging them with numbers, which is a prerequisite to follow them up in the proteinpaedia developed in our laboratory. The next step will be to retrieve the coding sequences from the existing partitioned cDNA library (BW 5147) as well as from thymocyte subtraction libraries. We predict that among those polypeptides with varying intensity, important regulatory proteins in thymus development will be found

Internal standard-based analysis of microarray data2—Analysis of functional associations between HVE-genes

In this work we apply the Internal Standard-based analytical approach that we described in an earlier communication and here we demonstrate experimental results on functional associations among the hypervariably-expressed genes (HVE-genes). Our working assumption was that those genetic components, which initiate the disease, involve HVE-genes for which the level of expression is undistinguishable among healthy individuals and individuals with pathology. We show that analysis of the functional associations of the HVE-genes is indeed suitable to revealing disease-specific differences. We show also that another possible exploit of HVE-genes for characterization of pathological alterations is by using multivariate classification methods. This in turn offers important clues on naturally occurring dynamic processes in the organism and is further used for dynamic discrimination of groups of compared samples. We conclude that our approach can uncover principally new collective differences that cannot be discerned by individual gene analysi

Integrated Epigenetics of Human Breast Cancer: Synoptic Investigation of Targeted Genes, MicroRNAs and Proteins upon Demethylation Treatment

The contribution of aberrant DNA methylation in silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations are reversible, it became of interest to determine the effects of the 5-aza-2'-deoxycytidine (DAC) demethylation therapy in breast cancer at different molecular levels

Internal standard-based analysis of microarray data2—Analysis of functional associations between HVE-genes

In this work we apply the Internal Standard-based analytical approach that we described in an earlier communication and here we demonstrate experimental results on functional associations among the hypervariably-expressed genes (HVE-genes). Our working assumption was that those genetic components, which initiate the disease, involve HVE-genes for which the level of expression is undistinguishable among healthy individuals and individuals with pathology. We show that analysis of the functional associations of the HVE-genes is indeed suitable to revealing disease-specific differences. We show also that another possible exploit of HVE-genes for characterization of pathological alterations is by using multivariate classification methods. This in turn offers important clues on naturally occurring dynamic processes in the organism and is further used for dynamic discrimination of groups of compared samples. We conclude that our approach can uncover principally new collective differences that cannot be discerned by individual gene analysis