Dataset Information

Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

ABSTRACT:

Background

Cluster analyses are used to analyze microarray time-course data for gene discovery and pattern recognition. However, in general, these methods do not take advantage of the fact that time is a continuous variable, and existing clustering methods often group biologically unrelated genes together.

Results

We propose a quadratic regression method for identification of differentially expressed genes and classification of genes based on their temporal expression profiles for non-cyclic short time-course microarray data. This method treats time as a continuous variable, therefore preserves actual time information. We applied this method to a microarray time-course study of gene expression at short time intervals following deafferentation of olfactory receptor neurons. Nine regression patterns have been identified and shown to fit gene expression profiles better than k-means clusters. EASE analysis identified over-represented functional groups in each regression pattern and each k-means cluster, which further demonstrated that the regression method provided more biologically meaningful classifications of gene expression profiles than the k-means clustering method. Comparison with Peddada et al.'s order-restricted inference method showed that our method provides a different perspective on the temporal gene profiles. Reliability study indicates that regression patterns have the highest reliabilities.

Conclusion

Our results demonstrate that the proposed quadratic regression method improves gene discovery and pattern recognition for non-cyclic short time-course microarray data. With a freely accessible Excel macro, investigators can readily apply this method to their microarray data.

SUBMITTER: Liu H

PROVIDER: S-EPMC1127068 | biostudies-literature | 2005 Apr

REPOSITORIES: biostudies-literature

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Publications

Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

Liu Hua H Tarima Sergey S Borders Aaron S AS Getchell Thomas V TV Getchell Marilyn L ML Stromberg Arnold J AJ

BMC bioinformatics 20050425

<h4>Background</h4>Cluster analyses are used to analyze microarray time-course data for gene discovery and pattern recognition. However, in general, these methods do not take advantage of the fact that time is a continuous variable, and existing clustering methods often group biologically unrelated genes together.<h4>Results</h4>We propose a quadratic regression method for identification of differentially expressed genes and classification of genes based on their temporal expression profiles for ...[more]

PMID: 15850479

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Project description:BackgroundTime-course microarray experiments produce vector gene expression profiles across a series of time points. Clustering genes based on these profiles is important in discovering functional related and co-regulated genes. Early developed clustering algorithms do not take advantage of the ordering in a time-course study, explicit use of which should allow more sensitive detection of genes that display a consistent pattern over time. Peddada et al. 1 proposed a clustering algorithm that can incorporate the temporal ordering using order-restricted statistical inference. This algorithm is, however, very time-consuming and hence inapplicable to most microarray experiments that contain a large number of genes. Its computational burden also imposes difficulty to assess the clustering reliability, which is a very important measure when clustering noisy microarray data.ResultsWe propose a computationally efficient information criterion-based clustering algorithm, called ORICC, that also takes account of the ordering in time-course microarray experiments by embedding the order-restricted inference into a model selection framework. Genes are assigned to the profile which they best match determined by a newly proposed information criterion for order-restricted inference. In addition, we also developed a bootstrap procedure to assess ORICC's clustering reliability for every gene. Simulation studies show that the ORICC method is robust, always gives better clustering accuracy than Peddada's method and saves hundreds of times computational time. Under some scenarios, its accuracy is also better than some other existing clustering methods for short time-course microarray data, such as STEM 2 and Wang et al. 3. It is also computationally much faster than Wang et al. 3.ConclusionOur ORICC algorithm, which takes advantage of the temporal ordering in time-course microarray experiments, provides good clustering accuracy and is meanwhile much faster than Peddada's method. Moreover, the clustering reliability for each gene can also be assessed, which is unavailable in Peddada's method. In a real data example, the ORICC algorithm identifies new and interesting genes that previous analyses failed to reveal.

Project description:BackgroundIn microarray gene expression profiling experiments, differentially expressed genes (DEGs) are detected from among tens of thousands of genes on an array using statistical tests. It is important to control the number of false positives or errors that are present in the resultant DEG list. To date, more than 20 different multiple test methods have been reported that compute overall Type I error rates in microarray experiments. However, these methods share the following dilemma: they have low power in cases where only a small number of DEGs exist among a large number of total genes on the array.ResultsThis study contrasts parallel multiplicity of objectively related tests against the traditional simultaneousness of subjectively related tests and proposes a new assessment called the Error Discovery Rate (EDR) for evaluating multiple test comparisons in microarray experiments. Parallel multiple tests use only the negative genes that parallel the positive genes to control the error rate; while simultaneous multiple tests use the total unchanged gene number for error estimates. Here, we demonstrate that the EDR method exhibits improved performance over other methods in specificity and sensitivity in testing expression data sets with sequence digital expression confirmation, in examining simulation data, as well as for three experimental data sets that vary in the proportion of DEGs. The EDR method overcomes a common problem of previous multiple test procedures, namely that the Type I error rate detection power is low when the total gene number used is large but the DEG number is small.ConclusionsMicroarrays are extensively used to address many research questions. However, there is potential to improve the sensitivity and specificity of microarray data analysis by developing improved multiple test comparisons. This study proposes a new view of multiplicity in microarray experiments and the EDR provides an alternative multiple test method for Type I error control in microarray experiments.

Project description:Accurate recognition and understating of human emotions is an essential skill that can improve the collaboration between humans and machines. In this vein, electroencephalogram (EEG)-based emotion recognition is considered an active research field with challenging issues regarding the analyses of the nonstationary EEG signals and the extraction of salient features that can be used to achieve accurate emotion recognition. In this paper, an EEG-based emotion recognition approach with a novel time-frequency feature extraction technique is presented. In particular, a quadratic time-frequency distribution (QTFD) is employed to construct a high resolution time-frequency representation of the EEG signals and capture the spectral variations of the EEG signals over time. To reduce the dimensionality of the constructed QTFD-based representation, a set of 13 time- and frequency-domain features is extended to the joint time-frequency-domain and employed to quantify the QTFD-based time-frequency representation of the EEG signals. Moreover, to describe different emotion classes, we have utilized the 2D arousal-valence plane to develop four emotion labeling schemes of the EEG signals, such that each emotion labeling scheme defines a set of emotion classes. The extracted time-frequency features are used to construct a set of subject-specific support vector machine classifiers to classify the EEG signals of each subject into the different emotion classes that are defined using each of the four emotion labeling schemes. The performance of the proposed approach is evaluated using a publicly available EEG dataset, namely the DEAPdataset. Moreover, we design three performance evaluation analyses, namely the channel-based analysis, feature-based analysis and neutral class exclusion analysis, to quantify the effects of utilizing different groups of EEG channels that cover various regions in the brain, reducing the dimensionality of the extracted time-frequency features and excluding the EEG signals that correspond to the neutral class, on the capability of the proposed approach to discriminate between different emotion classes. The results reported in the current study demonstrate the efficacy of the proposed QTFD-based approach in recognizing different emotion classes. In particular, the average classification accuracies obtained in differentiating between the various emotion classes defined using each of the four emotion labeling schemes are within the range of 73.8 % ? 86.2 % . Moreover, the emotion classification accuracies achieved by our proposed approach are higher than the results reported in several existing state-of-the-art EEG-based emotion recognition studies.

Dataset Information

Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

Background

Results

Conclusion

Publications

Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

Similar Datasets

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