- Research
- Open Access
Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells
- Margherita Mutarelli^{1, 2, 3},
- Luigi Cicatiello^{1, 3},
- Lorenzo Ferraro^{1},
- Olì MV Grober^{1, 3},
- Maria Ravo^{1},
- Angelo M Facchiano^{2},
- Claudia Angelini^{4} and
- Alessandro Weisz^{1, 3}Email author
https://doi.org/10.1186/1471-2105-9-S2-S12
© Mutarelli et al.; licensee BioMed Central Ltd. 2008
- Published: 26 March 2008
Abstract
Background
Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a ‘molecular picture’ of the cell state. On the other hand, the genomic responses to a pharmacological or hormonal stimulus are dynamic molecular processes, where time influences gene activity and expression. The potential use of the statistical analysis of microarray data in time series has not been fully exploited so far, due to the fact that only few methods are available which take into proper account temporal relationships between samples.
Results
We compared here four different methods to analyze data derived from a time course mRNA expression profiling experiment which consisted in the study of the effects of estrogen on hormone-responsive human breast cancer cells. Gene expression was monitored with the innovative Illumina BeadArray platform, which includes an average of 30-40 replicates for each probe sequence randomly distributed on the chip surface. We present and discuss the results obtained by applying to these datasets different statistical methods for serial gene expression analysis. The influence of the normalization algorithm applied on data and of different parameter or threshold choices for the selection of differentially expressed transcripts has also been evaluated. In most cases, the selection was found fairly robust with respect to changes in parameters and type of normalization. We then identified which genes showed an expression profile significantly affected by the hormonal treatment over time. The final list of differentially expressed genes underwent cluster analysis of functional type, to identify groups of genes with similar regulation dynamics.
Conclusions
Several methods for processing time series gene expression data are presented, including evaluation of benefits and drawbacks of the different methods applied. The resulting protocol for data analysis was applied to characterization of the gene expression changes induced by estrogen in human breast cancer ZR-75.1 cells over an entire cell cycle.
Keywords
- Slide Window Analysis
- BeadStudio Software
- Gene Regulation Event
- Time Series Gene Expression Data
- Microarray Experimental Design
Background
Estrogens (E2) are key regulators in many biological processes, along with a highly recognized role in breast cancer where they control key cellular functions by diffusing through the cell membrane and interacting with the estrogen receptors (ERs), transcription factors which play an important role in controlling multiple cellular processes mainly via changes in the expression of selected genes [1–3]. Complexity of the cellular responses to estrogen and their receptors can ideally be investigated only with comprehensive analytical approaches, including in particular gene expression profiling with microarrays [4, 5]. These technologies allow to assess at genome-wide scale changes in gene activity resulting, for example, from hormonal and pharmacological treatments or pathological and divergent physiological conditions. As changes in gene expression are driven by a dynamic process, the influence of time should not be neglected, but the use of this technique to study kinetics of gene expression changes has not been fully exploited yet. Indeed, few statistical methods are available which enable to fully evaluate time series. Most of the methods to identify differentially expressed genes adapt classical techniques originally designed for static experiments. This ‘static’ approaches have the disadvantage of not taking into account temporal relationship among samples, leading to results that are often invariant under permutation of the values representing different time points, thus ignoring the biological causality which can be inferred from the temporal response. They do not accurately consider the existing temporal structure in the data which can have as consequence a falsely calculated significance of the genes.
For example, the popular microarray analysis package SAM (Significance Analysis of Microarrays) [6] was recently adapted to handle time course data, by considering different time points as distinct groups; the ANOVA [7] approach can also be applied to time course experiments by treating the time variable as a particular experimental factor and other methods [8, 10], including the limma package [11] which uses linear models, follow similar approaches.
On the other hand, most classical time series algorithms, mainly used for signal processing, are quite rigid, including requirement of a large number of time-points, uniform sampling intervals and absence of replicated or missing data-points, which microarray experiments rarely meet.
Recently the time variable is starting to be much more considered in the analysis of regulation of gene expression, leading to new developments in the area of analysis of time-course microarray [9, 12, 13]. Due to the constraints in microarray data structure, however, the problem of detecting and estimating gene expression profiles becomes extremely challenging and robust statistical methodologies are still missing. On the other hand, very few large scale comparisons are available in order to illustrate benefits and drawbacks of current methodologies.
With the aim of setting up a workflow adapted for time course experiments, we tested the available methods tailored for time series analysis and established an analysis protocol to be used in subsequent experiments. The first method we considered introduces the time variable through a gene expression response curve which is expanded over the polynomial or B-spline basis with the coefficients estimated by the least squares procedure [14] (implemented in the software EDGE - Extraction of Differential Gene Expression [15]). The second method uses a novel multivariate empirical Bayes approach to rank genes in the order of interest from longitudinal replicated microarray time course experiments [16] (implemented in the Bioconductor [17] package timecourse). However, this last method does not consider time curves from a functional point of view, neither provides any cut-off to select statistically significant genes. The third method is a functional Bayesian approach in which each gene expression temporal profile is estimated globally by expanding it over an orthogonal basis [18] (implemented in the software BATS - Bayesian Analysis of Time Series [19]).
Our aim here, rather than to propose new methodologies, is to provide a detailed comparison of different methods which can be used as suitable protocol for analysis of time course gene expression data from microarray experiments.
Methods
Cell-lines cultures and array hybridizations
Human estrogen-responsive breast cancer cells (ZR-75.1) cultured in steroid-free medium for 4 days were stimulated with a mitogenic dose (10nM) of 17β-estradiol and RNA was extracted before or after 1, 2, 4, 6, 8, 12, 16, 20, 24, 28 and 32 hours hormonal stimulation. Cells were collected from multiple parallel cultures and pooled before RNA extraction as described before [4]. Hybridization reactions were performed with Illumina Human WG-6 BeadChips following manufacturer's protocols, in duplicate for each sample, except the reference sample (before stimulation - 0h) which was in quadruplicate and the 4h sample in triplicate. In the Illumina arrays the oligonucleotides are attached to microbeads which are then put onto microarrays using a random self-assembly mechanism [20]. Also, due to the small dimension of the beads, each bead-type (representing one probe for a total of 46713 sequences) is present in a number of the order of ≈ 30-40 copies, thus providing an internal technical replication that other platforms usually lack. In the present paper, we use the term ‘probe’ and ‘bead’ indifferently, since in each case we use as signal the mean value of each bead population of signals present on the array.
The complete datasets will be submitted to the public repository of microarray data ArrayExpress upon publication.
Pre-processing
Five different normalization algorithms were applied on data, three of them present in the chip manufacturer's analysis software BeadStudio and two of them performed using R/Bioconductor statistical environment [17, 21]. The average method simply adjusts the intensities of each signal so that the average signal of each array becomes the same. The rank invariant is very similar, the only difference is that the scaling factor is calculated only on a subset of rank-invariant genes and not on all genes [22]. The cubic spline is the only non-linear method present in the BeadStudio software, similar to an existing algorithm [23] and described in the software manual [22]. The quantile method [24] acts to uniform the quantile distribution of each array signal population and is widely used as standard in single-channel arrays [25]; it is available through the R/Bioconductor packages affy [26] or limma [11] and many other popular analysis software. Lumi[27] is a new method especially designed for Illumina BeadChips, based on a modification of the variance stabilizing normalization algorithm [28] to make use of the bead standard deviation associated to each signal, only available in this microarray platform.
After normalization, probe signals were checked for detection against negative controls with a BeadStudio internal algorithm and missing values were introduced to replace signals under the detection limit. Probes in which the reference sample had less than 3 out of 4 detected signals were filtered out. Then log 2 transformation was applied on data, except in the case of lumi which uses its own variance stabilizing transformation. Ratios of each signal against the average reference signal were calculated and probes with more than 15% missing values of the resulting time series were filtered out.
Time series analysis
The following sections contain a brief description of the methods used in this paper to perform the statistical analysis of a microarray experiment made in the course of time. For a detailed description of each method, we refer the reader to each method's reference. Some preliminary considerations are however necessary: the number of time points t^{(j)}, j = 1,…, n at which each sample is taken is relatively small (n ≈ 10) and the experimental design is not generally regular, with very few replicates at each time point (k_{ i }^{(j)} = 0,…, K, K = 1, 2 or 3); on the other hand a very large number of genes (N ≈ 10^{4}) are simultaneously measured, some data points might be missing due to technical error and the noise is usually not gaussian.
Sliding window analysis
We first extracted a list of differentially expressed genes at each time-point using the internal DiffScore test of BeadStudio software [22] by using thresholds of different stringency (a DiffScore of 20 and 30, corresponding respectively to a p-value of 0.01 and 0.001 of the underlying statistical test). We denoted as ‘differentially expressed’ genes those which were selected at least in three consecutive time-points. The limits of this procedure are the lack of statistical formalization and the fact that the fixed window does not account for irregularly spaced grid assigning to all points the same weight.
EDGE
The method proposed in Storey et al. [14] apply both to longitudinal and independent data. For each gene the effect of the treatment is modeled as a mathematical function and expanded over the polynomial or p-dimensional B-spline basis [s_{1} (t),…, s_{ p }(t)]. In our case data are not truly longitudinal since the biological source is a cell line, cultured in parallel, under identical and controlled conditions, hence the method is applied in its simplified version.
where $S{S}_{i}^{0}$ is the sum of squares of the residuals obtained from the null model, and $S{S}_{i}^{1}$ from the alternative model. However, Storey et al. [14] do not impose assumption of normality: the distribution of these statistics is treated as unknown and studied via bootstrap [29], which may require high computational cost. Finally, to account for the multiplicity of comparisons, the most significant curves are selected by controlling q-values using an FDR-like procedure [30].
This method is implemented in the user-friendly software EDGE [15]. We used the software with default parameter setting (increasing the number of iterations to 1000 in order to reduce the problem of the granularity of the p-values and to obtain more stable lists) and q-value thresholds of 0.01 and 0.001. The ‘K nearest neighbor’ (KNN) method [31] is provided to impute missing values, since the method itself does not account for missing data. In order to separate the effect of the method from the procedure to impute the missing values, we repeated the analysis both by filtering out all the genes with missing observations and by using the KNN method to impute them.
timecourse
This method applies the novel multivariate empirical Bayes approach described in Tai et al. [16] to rank genes in the order of interest from longitudinal replicated microarray time course experiments. Similarly to Storey et al. [14], timecourse can be applied both to the ‘one-sample’ and ‘two-sample’ case, however in the last case it is applicable only to data sets with identical time grids. On the other hand, differently from Storey et al. [14] where both longitudinal and independent sampling designs are accounted or from Angelini et al. [18] where only the independent sampling is considered, this method is designed for data where replicates are biologically meaningful, for example when a full series of time-points is drawn from the same individual (i.e., truly longitudinal). Indeed, biological samples are treated under the ‘fixed effects’ rather than the ‘random effects’ design model. Hence, since in this context one replicate is a full time curve (i.e, vector of size n), missing data are not allowed and the same number of arrays is required at any time point. On the other hand, different number of replicates are allowed between different genes.
where η > 0 is a scale parameter, ν > 0 and ν Λ < 0 are the degrees of freedom and scale matrix, respectively. Since conjugate priors are elicited on the unknown parameters, all computations for the posterior distributions and the form of the statistics are carried out in a analytical form. Moreover, the hyper-parameters, whose amount however increases with the number of time points, can be estimated from the data.
Finally, the Hotelling T^{2}-statistic is calculated and used to rank genes when the same number of replicates are available for all genes, while the M B-statistics is used when the number of replicates is not equal for all genes [16]. For further details on the statistics and on parameters estimation, we refer the interested reader to the original reference. Here we only note that, due to the way the data model was conceived, the quantitative information about the time measurements is not explicitly used by this method. The method is implemented in the timecourse R/Bioconductor package [32]. We applied the method using the first two replicates per time point, since the number of replicates has to be the same along the time curve. Also since missing values are not allowed, we repeated the analysis both by filtering out all the genes with missing observations and by using a KNN algorithm implementation present in R [33].
BATS
BATS (Bayesian Analysis of Time Series) software [19] is a newly-developed user friendly tool which implements the functional Bayesian approach described in Angelini et al. [18]. Although independently developed, the method appears to be a compromise between EDGE and timecourse. Indeed, similarly to EDGE, the method treats records as functional data, thus preserving causality and taking into account the temporal nature of data. Similarly to timecourse, the Bayesian approach is applied in the method at all stages of analysis, but the priors are elicited on the space of the function coefficients, hence the time variable enters in the model in explicit form trough the design matrix.
All parameters in the model are treated either as random variables or as nuisance parameters that are recovered from data. Noise variance σ^{2} is assumed to be random, σ^{2} ˜ ρ(σ^{2}) in order to account for possibly non-Gaussian errors which are quite common in microarray experiments.
Three different Bayesian models are contained in BATS providing the user a more flexible theoretical set-up to accommodate various types of error distributions, namely, all scale mixtures of a normal distribution: delta-type prior $\rho \left({\sigma}^{2}\right)=\delta \left({\sigma}^{2}-{\sigma}_{0}^{2}\right)$, the inverse Gamma prior ρ(σ^{2}) = IG(γ, b) and the exponential type prior $\rho \left({\sigma}^{2}\right)={c}_{\mu}{\sigma}^{{M}_{i}-1}{e}^{-{\sigma}^{2}\mu /2}$ which lead to normal, Student T and double-exponential errors, respectively. The choice of differentially expressed genes is made on the basis of Bayes Factors which are used for multiplicity control and are computed using the procedure described by Abramovich et al. [34]. Once significant genes are detected, the coefficients ${\widehat{c}}_{i}^{(l)}$ and, subsequently, the curve ${\widehat{\mu}}_{i}\left(t\right)$ are estimated by the posterior means. Hyperparameters π_{0} and ${\sigma}_{0}^{2}$, γ, b or μ are estimated from the data, or can be entered as known by the user. Gene specific parameters ${\tau}_{i}^{2}$ and L_{ i } are estimated by maximizing the marginal likelihood P(z_{ i }) and the posterior mean or mode of P(L_{ i }׀Z_{ i }), respectively.
The advantage of the Bayesian model described above is that since all priors are conjugate (see [18] for details), all posterior inference can be carried out analytically with very efficient computations.
The method is used for simultaneous estimation of the curves, as well as for ranking the curves (genes) according to their significance level. Moreover, significance testing of the curves is carried out by controlling the multiplicity of comparisons from a Bayesian perspective [34], providing an automatic cut-off. We performed the analysis by using two error models (the normal and the double-exponential) and a range of values of the parameter λ, which influences the prior degree of the polynomial curve estimated for each gene.
Simulations
To compare performances of EDGE, timecourse and BATS, we carried out a small simulation study by generating data with the Simulation utility of BATS. We generated data to mimic the structure of the real data set described above, with N = 10000, n = 11 and ${k}_{i}^{j}=2$ for all j = 1, …, 11 except ${k}_{i}^{4}=3$. In the data sets generated, 1000 or 2000 genes were randomly chosen to be “differentially expressed”, corresponding respectively to 10 % or 20 % of the total number of genes. The first scenario correspond to a case where relatively few genes are involved in the process, the second to a more strong respondence to the treatment. The values of 1000 and 2000 where chosen from the prior belief on behavior of the real data experiments. The remaining 9000 or 8000 curves were set to identical zero.
For each significant curve, the Simulation utility samples the degree of the polynomial ${L}_{i}^{true}$ from a discrete uniform distribution in [1, L_{max}], with L_{max} = 6 (in contrast to the truncated Poisson that is used in fitting the model). Polynomials of degree zero are excluded since a nonzero constant signal is questionable from a biological point of view. Coefficients c_{ i } where randomly sampled from $N\left(0,{\sigma}^{2}{\tau}_{i}^{2}{Q}_{i}^{-1}\right)$. Matrix Q_{ i } is set to ${Q}_{i}=\text{diag}\left({1}^{2{\nu}_{i}},{2}^{2{\nu}_{i}},\mathrm{...},{L}_{i}^{2{\nu}_{i}}\right)$ where ν_{ i } ∼ U([0,1]) and ${\tau}_{i}^{2}$ was sampled uniformly in order to produce the signal-to-noise ratio (SNR) in the interval between 2 and 6. Under this set up we can mimic both weak and strong signals and different signal regularity (which is not accounted explicitly by any of the models). Furthermore, since is known that noise on microarray date has heavier tails than gaussian, we performed simulations under three scenarios of i.i.d. noise: normal N(0, σ^{2}) and Student T with 5 or 3 degrees of freedom (indicated as T 5 and T 3, respectively). Student noise was rescaled to have the same variance σ^{2} of the normal case (σ = 0.33, the estimated value for the real data set).
In addition, very large values (with a threshold of 5) were filtered out and substituted with missing values, mimicking real data preprocessing where unreliable values are eliminated.
For each kind of noise and number of true signals we generated 5 data-set, averaging the results. Analysis of simulated data was performed with the three methods with the same choice of parameters used in the real data analysis: EDGE q-value 0.01 and 0.001; BATS error model normal and double exponential and λ = 9 and λ = 12; with timecourse we chose the first genes in the ranked list corresponding to the same number of the genes selected by BATS on the same dataset, to evaluate the number of false positives and false negatives.
Cluster analysis
Cluster analysis on the final list of gene profiles significantly affected by estrogen stimulation was performed using a Bayesian functional based software, Splinecluster [35]. The method proposes a hierarchical cluster approach, where the number of cluster is automatically selected by maximizing the marginal distribution. However, it is recommended both for computational and for practical point of view to apply the method only on the relevant subset of genes, instead of the whole dataset of genes. Here, similarly to BATS, the gene profiles are also represented by expansions over a certain basis and the normal-inverse gamma prior is imposed on the unknown coefficients. The number of clusters and cluster participation are also treated as random, leading to a full Bayesian model. Since the method does not address many of the issues which we treat in the Results and discussion Section, we processed the selected data matrix by filtering out missing data points and by averaging the replicates at each time point.
Results and discussion
Experimental design of the experiment and its implications
We present the analysis performed on a time series of microarray data from breast cancer cells treated with estrogens. Our experimental design is formalized in a ‘one sample’ statistical model with a time series, in which replicated arrays for each time-point are technical replicates, with no special relationships between each other. We also have unequally spaced sampling intervals (1h between the first two time-points, 2h till the time-point of 8h and 4h till the end of the series) and 2 replicates at each time-point, except one case (4h) in which we have 3 replicates. This data structure has quite common features in microarray experimental designs: a number of replicates barely sufficient to get statistically significant results, unequal number of replicates which may be due to technical needs or reasons of biological interest. For example, the higher detail in the first part of the curve reflects a greater interest from a biological point of view in the earlier responses to hormone treatment with respect to the rest of the time series. Some difficulties may arise in analyzing data presenting features like these, both for a static analysis approach and with a longitudinal method. In fact, for a static method of comparison treated/non treated, performed point-by-point, the number of replicates of individual time-points is lower than the required minimum of most standard tests. This limited number of replicates is justified by the time-series analysis: since we are interested in the whole profile, we don't need absolute precision in each time point comparison but rather we need to take advantage of the temporal structure of the data and use all information available along the time in order to make appropriate and robust inference.
Pre-processing
We evaluated the effect of different normalization algorithms in terms of overlap between the selected gene lists produced with the time-series analysis methods used. After inspection of normalized data, the cubic spline method was discarded since the data produced was not correctly normalized between the arrays (see Additional file 1), thus requiring further manipulation on data that we decided not to apply. The better overlap was noted between quantile and lumi normalization, with average being the best performing algorithm among the ones present in BeadStudio software.
After the filtering step, the genes left for the analysis were 9593, of which 1261 (13.2%) had between 1 and 4 missing values.
Time series analysis
Sliding window analysis
Comparison of the selected gene lists obtained with different methods of selection.
Numbers indicate the genes obtained by pairwise intersection of different methods of selection. In bold are the selected gene lists for each method.
Sliding window 20^{1} | Sliding window 30^{1} | EDGE 0.01^{2} | EDGE 0.001^{2} | BATS #1^{3} | BATS #2^{4} | timecourse 1000^{5} | timecourse 1500^{5} | |
---|---|---|---|---|---|---|---|---|
Sliding window 20^{1} | 1563 | 997 | 1126 | 667 | 903 | 1069 | 140 | 209 |
Sliding window 30^{1} | 997 | 825 | 540 | 690 | 797 | 85 | 128 | |
EDGE 0.01^{2} | 2595 | 1145 | 936 | 1086 | 232 | 343 | ||
EDGE 0.001^{2} | 1145 | 590 | 659 | 104 | 154 | |||
BATS #1^{3} | 1478 | 1397 | 157 | 157 | ||||
BATS #2^{4} | 1660 | 232 | 243 | |||||
timecourse 1000^{5} | 1000 | 1000 | ||||||
timecourse 1500^{5} | 1500 |
EDGE
EDGE is distributed as a stand-alone software and, although relying on R [21], it silently uses it in the background, so that the user does not need to know the language to use it but only interacts with a graphical interface. It also has some useful utilities to inspect the input data, such as the possibility to make boxplots, to check the presence of missing data and to impute them with the KNN algorithm. The results are highly robust to changing normalizations (80-96% overlap among all the four methods) except for the case of rank invariant normalization, with which the number of significant genes drops unexpectedly with respect to the others. We obtained similar results both by filtering out missing data and by imputing them. As compared with the other methods, on real data EDGE selects a surprisingly much longer list of genes (Table 1). Moreover, we observed that, even though we increased the number of permutations, due to the granularity problem, genes with the same q-value are too many, since for example the first 67 (average norm.), 44 (lumi) or 85 (quantiles) genes all result as ‘first rank’ genes with the same q-value. To reduce granularity one should further increase the number of permutations, but then as a consequence the computational cost would also increase, thus making the method less convenient to use.
timecourse
timecourse [32] is a package distributed with Bioconductor [17], thus requiring knowledge of the statistical environment R [21], which is both an advantage for those familiar with this language, since it is very quick to install and use new packages, but it can be unfriendly for biologists. Similarly to EDGE, we found very similar results both when filtering out genes with missing observations and when imputing them. This method only ranks in order of significance the input gene list without providing an automatic or suggested cut-off to determine which genes are significant. For this reason, on real data we selected the first 1000 and 1500 genes of the rank ordered lists to compare results among normalizations and with the other methods. Surprisingly, we found a very low overlap both between the ordered lists prepared with different normalizations and with lists produced with other methods (Table 1). It is worth mentioning that our dataset contains only technical (indistinguishable) replicates, thus the method could not take advantage of the replicate identification, nonetheless the difference with the other methods and above all between data normalized with different methods is difficult to explain.
BATS
Comparison of methods
Simulation study
Simulation study.
Datasets generated with 1000 true signals, with three different noise models. Results were averaged over 5 datasets.
Noise model N | Noise model T5 | Noise model T3 | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Method | Rej.^{4} | Corr.^{5} | FDR^{6} | FNR^{7} | Rej.^{4} | Corr.^{5} | FDR^{6} | FNR^{7} | Rej.^{4} | Corr.^{5} | FDR^{6} | FNR^{7} |
EDGE^{1} 0.01 | 383.8 | 382.4 | 0.004 | 0.064 | 405.6 | 403.4 | 0.005 | 0.062 | 462.6 | 460.8 | 0.004 | 0.057 |
EDGE^{1} 0.001 | 207.8 | 207.4 | 0.002 | 0.081 | 183.6 | 183.6 | 0.000 | 0.083 | 187 | 187 | 0.000 | 0.083 |
timecourse ^{2} | 775.6 | 733.4 | 0.054 | 0.029 | 794.4 | 690.6 | 0.131 | 0.034 | 869.8 | 733.4 | 0.157 | 0.029 |
BATS^{3} N, 9 | 775.6 | 775.6 | 0.000 | 0.024 | 794.4 | 782.6 | 0.015 | 0.024 | 869.8 | 803.4 | 0.076 | 0.022 |
BATS^{3} N, 12 | 775.4 | 775.4 | 0.000 | 0.024 | 794.2 | 782.4 | 0.015 | 0.024 | 869 | 802.6 | 0.076 | 0.022 |
BATS^{3} D, 9 | 753.2 | 753.2 | 0.000 | 0.027 | 774.8 | 762.8 | 0.015 | 0.026 | 875.4 | 793.4 | 0.094 | 0.023 |
BATS^{3} D, 12 | 745.8 | 745.8 | 0.000 | 0.027 | 768.4 | 756.4 | 0.016 | 0.026 | 871.6 | 789.2 | 0.095 | 0.023 |
Simulation study.
Datasets generated with 2000 true signals, with three different noise models. Results were averaged over 5 datasets.
Noise model N | Noise model T5 | Noise model T3 | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Method | Rej.^{4} | Corr.^{5} | FDR^{6} | FNR^{7} | Rej.^{4} | Corr.^{5} | FDR^{6} | FNR^{7} | Rej.^{4} | Corr.^{5} | FDR^{6} | FNR^{7} |
EDGE^{1} 0.01 | 928.4 | 921.8 | 0.007 | 0.119 | 953.4 | 948 | 0.006 | 0.1163 | 1054.6 | 1048.2 | 0.006 | 0.106 |
EDGE^{1} 0.001 | 519.6 | 519.6 | 0.000 | 0.156 | 526 | 526 | 0.000 | 0.1556 | 544.6 | 544.6 | 0.000 | 0.154 |
timecourse ^{2} | 1386 | 1380 | 0.004 | 0.072 | 1396 | 1319 | 0.055 | 0.0791 | 1461 | 1384 | 0.052 | 0.072 |
BATS^{3} N, 9 | 1385.8 | 1385.8 | 0.000 | 0.071 | 1395.8 | 1391 | 0.003 | 0.0708 | 1460.6 | 1435 | 0.018 | 0.066 |
BATS^{3} N, 12 | 1382 | 1382 | 0.000 | 0.072 | 1393.4 | 1388.6 | 0.003 | 0.0710 | 1459.6 | 1433 | 0.018 | 0.066 |
BATS^{3} D, 9 | 1386 | 1386 | 0.000 | 0.071 | 1407.2 | 1403.4 | 0.003 | 0.0694 | 1510.2 | 1477.4 | 0.022 | 0.062 |
BATS^{3} D, 12 | 1368.2 | 1368.2 | 0.000 | 0.073 | 1384.2 | 1380.4 | 0.003 | 0.0719 | 1489.8 | 1457 | 0.022 | 0.064 |
For what concerns EDGE, we observe a quite conservative behavior (it has a higher FNR with respect the other methods) which is not preserved on the analysis of real data. This might be due to the bootstrap technique applied to estimate the parameters.
In the case of timecourse, we note a higher consistency with the other methods, in spite of its strikingly different results when applied on real data. It is not surprising to observe that the methods performed differently on real data with respect to simulated data, since any simulation has implicit assumptions which may or may not be verified on experimental datasets. Apparently, a more irregular noise distribution on real data has arisen opposite problems to EDGE and timecourse in detecting gene expression signals over the noise, while on the contrary it does not affect the performance of BATS significantly.
Real data analysis
When several methods are compared on experimental data, there is no clear and well accepted way to compare performance of each approach and the final choice usually depends upon several considerations. We thus first investigated the robustness of each procedure in terms of user selected parameters and different normalization procedures (data not shown). In Table 1 are reported the results relative to the gene lists selected by each of the procedures described above, all normalized according to the average method. As shown, the less rigorous sliding window approach as well as EDGE and BATS have a satisfying overlap among the gene list they select. We then considered the different methods from a statistical point of view, analyzing benefits and drawbacks.
Sliding windows is of course the less statistically rigorous, it does not take into account unequally spaced time points or missing data nor provides a global measure of significance for the whole time series. On the other hand, this is very intuitive and computationally inexpensive, and may be useful to detect local changes.
EDGE, on the other hand, suffers for the problem of the granularity of p-values which can be only partially solved by increasing the number of iterations, although at the price of a high computational cost, which can become prohibitive for large dataset. Moreover, the choice of an appropriate threshold may become problematic, since small changes lead to remarkable differences in the selected gene lists. Furthermore, EDGE assumes the same degree in the functional expansion of each gene and, as a consequence, it may lack in adaptation. It has, however, the merit of being the first tool to formalize the problem of selection by a functional approach.
timecourse is mainly designed for a slightly different problem, hence its use in the context considered here does not allow to take complete advantage of the methods itself. Moreover, similarly to EDGE, timecourse does not account for missing data, requiring the user to filter out incomplete datasets, missing time points, or to force the user to employ preliminary procedures in order to impute them. Furthermore, this method does not provide an automatic cut-off for selecting significant genes, nor uses the quantitative ‘time’ information in an explicit way.
Hence, we found BATS more appropriate for this experimental setting, since it automatically accounts for various technical difficulties which arise in microarray time course experiments, such as limited number of observations, non uniform sampling intervals or missing/multiple records, all conditions which are not completely addressed by the above mentioned alternative methods. Moreover, since BATS does not require bootstrap and posterior inference can be evaluated in closed form, and it is applicable also to the larger datasets that are becoming more widely used due to microarray technology improvements and diffusion. Furthermore, it has the merit of providing an estimate of the significant expression profile, which is not explicitly provided by any of the other methods, while being also very flexible, capable of handling gene specific variance and, using the Bayesian paradigm, allowing better adaptation of the estimates to the underlying data.
Cluster analysis
Conclusions
Microarray experiments enable to study at genome-wide level the dynamics of gene regulation events. Since thousands of genes are spotted in modern platforms, the amount of data provided is relevant, hence it is important to have an automatic, statistically robust, computationally fast and flexible procedure to select gene expression profiles which show significant changes in time.
We tested different methods tailored for analyzing data derived from time-course microarray experiments, which can be modeled under a ‘one sample’ framework, in order to find the most appropriate analysis pipeline to use in future experiments.
We evaluated advantages and limits of each method assessed, in terms of usability, computational burden, flexibility to characteristics of microarray experimental designs, robustness to normalizations and overlap with the other methods. We have found an analysis pipeline of R/Bioconductor preprocessing and then selection of significant genes with BATS to be the most appropriate in the ‘one sample’ case. Selected genes can then be clustered with Splinecluster [35], which is a method which uses a functional approach, coherently with the selection procedure used.
To validate the biological significance of the gene expression profiles and gene clusters here identified, these were compared with the results we obtained previously in estrogen-stimulated ZR-75.1 cells under identical experimental conditions [4]. The majority of the genes in common among the two lists showed very similar/identical pattern of expression. This is evident, for example, when comparing in Additional file 2 and Cicatiello et al. [4] the data relative to: EGR1 (early growth response 1: cluster 1), ZNF217 (zinc finger protein 217: cluster 1), MYC (c-myc: cluster 32), FOS (c-fos: cluster 32), TFF1 (trefoil factor 1: cluster 17), CCND1 (cyclin D1: cluster 18), CCNA2 (cyclin A2: cluster 19) and CCNB1 (cyclin B1: cluster 19). All these genes are known target of ERs, while their activity relates to regulation of cell cycle phasing. The pattern of induction/repression of these genes by estrogen over time (see also Figure 1), as identified with the method here described, perfectly corresponds to their known biological role in these cells, providing a strong biological confirmation of the reliability of the gene selection method proposed.
Declarations
Acknowledgements
Research supported by: MIUR (PRIN 2005063915_003 and 2006069030_003), UE (CRESCENDO IP, contract nr. LSHM-CT2005-018652), Second University of Napoli, CNR-Bioinformatics Project, Oncoproteomics Project Conv.n.527B/2A/10 and AIRC (Italian Association for Cancer Research), Ph.D. Programs: ‘Pathology of Cellular Signal Transduction’ of the Second University of Naples (OMVG) and ‘Toxicology, Oncology and Molecular Pathology’ of the University of Cagliari (MR).
This article has been published as part of BMC Bioinformatics Volume 9 Supplement 2, 2008: Italian Society of Bioinformatics (BITS): Annual Meeting 2007. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105/9?issue=S2
Authors’ Affiliations
References
- Weisz A: Estrogen regulated genes. In Handbook of Experimental Pharmacology, Volume 135/I: Estrogens and Antiestrogens. Edited by: Oettel M, Schillinger E. Berlin-Heidelberg-New York: Springer Verlag; 1999:127–151.Google Scholar
- Weisz A: New insights on estrogen action from gene expression profiling. In Signal Transduction and Neoplastic Transformation in Endocrine Systems: Molecular mechanisms and clinical aspects, Volume 211. Roma: Atti dei Convegni Lincei, Bardi; 2005:143–153.Google Scholar
- Weisz A, Addeo R, Altucci L, Battista T, Boccia V, Cancemi M, Cicatiello L, Germano D, Mancini A, Pacilio C, Bresciani F: Molecular mechanisms for estrogen control of cell cycle progression during G1. In Sex Steroid Hormone Action. Edited by: Edited by Kuramoto H, Gurpide E, Tokyo. Churchill Livingstone Japan; 1996:1–16.Google Scholar
- Cicatiello L, Scafoglio C, Altucci L, Cancemi M, Natoli G, Facchiano A, Iazzetti G, Calogero R, Biglia N, De Bortoli M, Sfiligol C, Sismondi P, Bresciani F, Weisz A: A genomic view of estrogen actions in human breast cancer cells by expression profiling of the hormone-responsive transcriptome. J Mol Endocrinol 2004, 32: 719–775.View ArticlePubMedGoogle Scholar
- Scafoglio C, Ambrosino C, Cicatiello L, Altucci L, Ardovino M, Bontempo P, Medici N, Molinari AM, Nebbioso A, Facchiano A, Calogero R, Elkon R, Menini N, Ponzone R, Biglia N, Sismondi P, De Bortoli M, Weisz A: Comparative gene expression profiling reveals partially overlapping but distinct genomic actions of different antiestrogens in human breast cancer cells. J. Cell. Biochem. 2006, 98: 1163–1184.View ArticlePubMedGoogle Scholar
- Tusher V, Tibshirani R, Chu C: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98: 5116–5121.PubMed CentralView ArticlePubMedGoogle Scholar
- Kerr MK, Martin M, Churchill GA: Analysis of variance for gene expression microarray data. J Comput Biol 2000, 7: 819–837.View ArticlePubMedGoogle Scholar
- Park T, Yi SG, Lee S, Lee SY, Yoo DH, Ahn JI, Lee YS: Statistical tests for identifying differentially expressed genes in time course microarray experiments. Bioinformatics 2003, 19: 694–703.View ArticlePubMedGoogle Scholar
- Conesa A, Nueda MJ, Ferrer A, Talon M: MaSigPro: a method to identify significantly differential expression profiles in time-course microarray-experiments. Bioinformatics 2006, 22: 1096–1102.View ArticlePubMedGoogle Scholar
- Di Camillo B, Sanchez-Cabo F, Toffolo G, Nair SK, Trajanosky Z, Cobelli C: A quantization method based on threshold optimization for microarray short time series. BMC Bioinformatics 2005, 6(Suppl 4):S11.PubMed CentralView ArticlePubMedGoogle Scholar
- Smyth GK: Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor Edited by: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, Springer. 2005, 397–420.View ArticleGoogle Scholar
- De Hoon MJL, Imoto S, Miyano S: Statistical analysis of a small set of time-ordered gene expression data using linear splines. Bioinformatics 2002, 18: 1477–1485.View ArticlePubMedGoogle Scholar
- Bar-Joseph Z: Analyzing time series gene expression data. Bioinformatics 2004, 20: 2493–2503.View ArticlePubMedGoogle Scholar
- Storey JD, Xiao W, Leek JT, Tompkins RG, Davis RW: Significance analysis of time course microarray experiments. Proc Natl Acad Sci U S A 2005, 102: 12837–12842.PubMed CentralView ArticlePubMedGoogle Scholar
- Leek J, Monsen E, Dabney A, Storey J: EDGE: extraction and analysis of differential gene expression. Bioinformatics 2006, 22: 507–508.View ArticlePubMedGoogle Scholar
- Tai YC, Speed TP: A multivariate empirical Bayes statistic for replicated microarray time course data. Ann Statist 2006, 34: 2387–2412.View ArticleGoogle Scholar
- Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini A, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5: R80-R80.PubMed CentralView ArticlePubMedGoogle Scholar
- Angelini C, De Canditiis D, Mutarelli M, Pensky M: A Bayesian Approach to Estimation and Testing in Time-course Microarray Experiments. Stat Appl Genet Mol Biol 2007, 6():Article24.PubMedGoogle Scholar
- Angelini C, Cutillo L, De Canditiis D, Mutarelli M, Pensky M: BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments. Rapp. Tech. IAC-CNR 331–07 2007.Google Scholar
- Gunderson KL, Kruglyak S, Graige MS, Garcia F, Kermani BG, Zhao C, Che D, Dickinson T, Wickham E, Bierle J, Doucet D, Milewski M, Yang R, Siegmund C, Haas J, Zhou L, Oliphant A, Fan J, Barnard S, Chee MS: Decoding randomly ordered DNA arrays. Genome Res. 2004, 14: 870–877.PubMed CentralView ArticlePubMedGoogle Scholar
- Everitt B, Hothorn T: A Handbook of Statistical Analyses Using R. In In Genome Res.. Boca Raton, FL: Chapman & Hall/CRC 2006; . [ISBN 1–584–88539–4]. [http://cran.r-project.org/web/packages/HSAUR/index.html]Google Scholar
- Illumina Inc In BeadStudio User Guide. San Diego, USA 2004; 2005. . [Doc. 11179632 Rev. B]. [http://www.illumina.com]
- Workman C, Jensen L, Jarmer H, Berka R, Gautier L, Nielser H, Saxild H, Nielsen C, Brunak S, Knudsen S: A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol 2002, 3: research0048-research0048.PubMed CentralView ArticlePubMedGoogle Scholar
- Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 2003, 19: 185–193.View ArticlePubMedGoogle Scholar
- Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P: Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res 2005, 33: 5914–5923.PubMed CentralView ArticlePubMedGoogle Scholar
- Gautier L, Cope L, Bolstad BM, Irizarry RA: affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20: 307–315.View ArticlePubMedGoogle Scholar
- Du P, Kibbe W, Lin S: Using lumi, a package processing Illumina Microarray.2007. [http://www.bioconductor.org]Google Scholar
- Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M: Variance Stabilization Applied to Microarray Data Calibration and to the Quantification of Differential Expression. Bioinformatics 2002, 18(Suppl 1):S96-S104.View ArticlePubMedGoogle Scholar
- Efron B, Tibshirani R: An Introduction to the Bootstrap. Boca Raton, FL: Chapman and Hall; 1993.View ArticleGoogle Scholar
- Storey J, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 2003, 100: 9440–9445.PubMed CentralView ArticlePubMedGoogle Scholar
- Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB: Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17: 520–525.View ArticlePubMedGoogle Scholar
- Tai Y, Speed T: Statistical analysis of microarray time course data. In DNA Microarrays. Edited by: Edited by Nuber U. Taylor and Francis; 2005. [ISBN 9780415358668]Google Scholar
- Hastie T, Tibshirani R, Sherlock G, Eisen M, Brown P, Botstein D: Imputing Missing Data for Gene Expression Arrays. Stanford University Statistics Department Technical report 1999. . [http://www-stat.stanford.edu/~hastie/Papers/missing.pdf]Google Scholar
- Abramovich F, Angelini C: Bayesian Maximum a Posteriori Multiple Testing Procedure. Sankhya - The Indian Journal of Statistics 2006, 68: 436–460.Google Scholar
- Heard N, Holmes C, Stephen D: A quantitative study of gene regulation involved in the Immune response of Anopheline Mosquitoes: An application of Bayesian hierarchical clustering of curves. J. Amer. Stat. Soc. 2006, 101: 18–29.View ArticleGoogle Scholar
- The MathWorks I In Getting Started with MATLAB 7. The MathWorks, Inc., Natick, USA 2007; [http://www.mathworks.com]
- Cicatiello L, Addeo R, Sasso AR, Altucci L, Belsito Petrizzi V, Borgo R, Cancemi M, Caporali S, Caristi S, Scafoglio C, Teti D, Bresciani F, Perillo B, Weisz A: Estrogens promote persistent G1 activation of the CCND1 gene by inducing transcriptional de-repression via c-Jun/c-Fos/ER complex assembly to a distal regulatory element and recruitment of cyclin D1 to its own gene promoter. Mol. Cell. Biol. 2004, 24: 7260–7274.PubMed CentralView ArticlePubMedGoogle Scholar
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