Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
BackgroundThe increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval.ResultsWe extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified.ConclusionsThe extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsa.
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
MOTIVATION Local similarity analysis of biological time series data helps elucidate the varying dynamics of biological systems. However, its applications to large scale high-throughput data are limited by slow permutation procedures for statistical significance evaluation. RESULTS We developed a theoretical approach to approximate the statistical significance of local similarity analysis based on the approximate tail distribution of the maximum partial sum of independent identically distributed (i.i.d.) random variables. Simulations show that the derived formula approximates the tail distribution reasonably well (starting at time points > 10 with no delay and > 20 with delay) and provides P-values comparable with those from permutations. The new approach enables efficient calculation of statistical significance for pairwise local similarity analysis, making possible all-to-all local association studies otherwise prohibitive. As a demonstration, local similarity analysis of human microbiome time series shows that core operational taxonomic units (OTUs) are highly synergetic and some of the associations are body-site specific across samples. AVAILABILITY The new approach is implemented in our eLSA package, which now provides pipelines for faster local similarity analysis of time series data. The tool is freely available from eLSA's website: http://meta.usc.edu/softs/lsa. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT fsun@usc.edu.
neural network sensor network machine learning artificial neural network support vector machine deep learning time series data mining support vector vector machine wavelet transform data analysi deep neural network neural network model hidden markov model regression model deep neural anomaly detection gene expression data base generative adversarial network generative adversarial time series datum adversarial network experimental datum fourier series nearest neighbor support vector regression time series analysi missing datum data based moving average gene expression datum time series model series analysi lyapunov exponent series datum outlier detection dynamic time warping time series forecasting data mining algorithm panel datum time series prediction series model multivariate time series finite time unit root dynamic time linear and nonlinear series forecasting time warping distance measure financial time series series prediction integrated moving average experimental comparison multivariate time financial time dependent variable chaotic time series nonlinear time vegetation index nonlinear time series arima model fuzzy time large time anomaly detection method fuzzy time series chaotic time autoregressive integrated moving time series based air pollutant time series classification representation method fokker-planck equation series representation similarity analysi series classification univariate time series time series clustering unsupervised anomaly detection periodic pattern nearest neighbor classification time series dataset series data mining time series regression anomaly detection approach time series database series clustering observed time series forecasting time series local similarity long time series time series similarity series database fmri time series complex time indian stock market time series representation symbolic aggregate approximation complex time series forecasting time series data set series similarity fmri time time series anomaly large time series series data analysi series anomaly detection analyzing time series expression time series interrupted time series ucr time series time correction modeling time series clustering time series mining time series interrupted time series data based fourier series representation simple exponential smoothing early classification forecast time series time series subsequence sensor networks pose distributed index piecewise constant approximation quality time series mining time microarray time series incomplete time series massive time series large-scale time series analysing time series microarray time neural time series mri time neural time series data generated time series experiment visualizing time series called time series data set