A novel data mining method to identify assay-specific signatures in functional genomic studies

BACKGROUND: The highly dimensional data produced by functional genomic (FG) studies makes it difficult to visualize relationships between gene products and experimental conditions (i.e., assays). Although dimensionality reduction methods such as principal component analysis (PCA) have been very useful, their application to identify assay-specific signatures has been limited by the lack of appropriate methodologies. This article proposes a new and powerful PCA-based method for the identification of assay-specific gene signatures in FG studies. RESULTS: The proposed method (PM) is unique for several reasons. First, it is the only one, to our knowledge, that uses gene contribution, a product of the loading and expression level, to obtain assay signatures. The PM develops and exploits two types of assay-specific contribution plots, which are new to the application of PCA in the FG area. The first type plots the assay-specific gene contribution against the given order of the genes and reveals variations in distribution between assay-specific gene signatures as well as outliers within assay groups indicating the degree of importance of the most dominant genes. The second type plots the contribution of each gene in ascending or descending order against a constantly increasing index. This type of plots reveals assay-specific gene signatures defined by the inflection points in the curve. In addition, sharp regions within the signature define the genes that contribute the most to the signature. We proposed and used the curvature as an appropriate metric to characterize these sharp regions, thus identifying the subset of genes contributing the most to the signature. Finally, the PM uses the full dataset to determine the final gene signature, thus eliminating the chance of gene exclusion by poor screening in earlier steps. The strengths of the PM are demonstrated using a simulation study, and two studies of real DNA microarray data – a study of classification of human tissue samples and a study of E. coli cultures with different medium formulations. CONCLUSION: We have developed a PCA-based method that effectively identifies assay-specific signatures in ranked groups of genes from the full data set in a more efficient and simplistic procedure than current approaches. Although this work demonstrates the ability of the PM to identify assay-specific signatures in DNA microarray experiments, this approach could be useful in areas such as proteomics and metabolomics

Use of Discrete-Time Forecast Modeling to Enhance Feedback Control and Physically Unrealizable Feedforward Control with Applications

When the manipulated variable (MV) has significantly large time delay in changing the control variable (CV), use of the currently measured CV in the feedback error can result in very deficient feedback control (FBC). However, control strategies that use forecast modeling to estimate future CV values and use them in the feedback error have the potential to control as well as a feedback controller with no MV deadtime using the measured value of CV. This work evaluates and compares FBC algorithms using discrete-time forecast modeling when MV has a large deadtime. When a feedforward control (FFC) law results in a physically unrealizable (PU) controller, the common approach is to use approximations to obtain a physically realizable feedforward controller. Using a discrete-time forecast modeling method, this work demonstrates an effective approach for PU FFC. The Smith Predictor is a popular control strategy when CV has measurement deadtime but not MV deadtime. The work demonstrates equivalency of this discrete-time forecast modeling approach to the Smith Predictor FBC approach. Thus, this work demonstrates effectiveness of the discrete-time forecast modeling approach for FBC with MV or DV deadtime and PU FFC

Development of a Model-Based Noninvasive Glucose Monitoring Device for Non-Insulin Dependent People

Continuous-time glucose monitoring (CGM) effectively improves glucose control, as oppose to infrequent glucose measurements (i.e. using Lancet Meters), by providing frequent blood glucose concentration (BGC) to better associate this variation with changes in behavior. Currently, the most widely used CGM devices rely on a sensor that is inserted invasively under the skin. Because of the invasive nature and also the replacement cost of sensors, the primary users of current CGM devices are insulin dependent people (type 1 and some type 2 diabetics). Most non-insulin dependent diabetics use only lancet glucose measurements. The ultimate goal of this research is the development of CGM technology that overcomes these limitations (i.e. invasive sensors and their cost) in an effort to increase CGM applications among non-insulin dependent people. To meet this objective, this preliminary work has developed a methodology to mathematically infer BGC from measurements of non-invasive input variables which can be thought of as a “virtual” or “soft” sensor approach. In this work virtual sensors are developed and evaluated on 20 subjects using four BGC measurements per day and eight input variables representing meals, activity, stress, and clock time. Up to four weeks of data are collected for each subject. One evaluation consists of 3 days of training and up to 25 days of testing data. The second one consists of one week of training, one week of validation, and 2 weeks of testing data. The third one consists two weeks of training, one week of validation and one week of testing data. Model acceptability is determined on an individual basis based on the fitted correlation to CGM testing data. For 3 day, 1 week, and 2 weeks training studies, 35%, 55% and 65% of the subjects, respectively, met the Acceptability Criteria that we established based on the concept of usefulness