BACKGROUND
time-course gene expression data are often measured to study dynamic biological systems and gene regulatory networks.
array technologies have made it straightforward to monitor the expression pattern of thousands of genes simultaneously.
the challenge now is to interpret such massive data sets.
the first step is to extract the fundamental patterns of gene expression inherent in the data.
gene-expression levels can be monitored with cdna or oligonucleotide chips over a time-course for a temporal process.
following a microarray time series experiment, a key challenge is to extract the continuous representation of all genes throughout the time-course.
identifying significant or differentially expressed genes is challenging because different genes may have different profiles, and because of the noise present in time series expression data.
a comprehensive review about time series expression data analysis and the related computational challenges may be found in  <cit> .
microarrays have recently been used for the purpose of monitoring expression levels of thousands of genes simultaneously and for identifying genes that are differentially expressed.
with the number of inferences made in the analysis of microarray data, it is natural to be concerned about multiple testing.
this problem of multiplicity can be dealt with by controlling the false discovery rate   <cit> .
in the past decade, many approaches to gene selection have been considered including a two sample t-test  <cit> , a regression approach  <cit> , and a mixture model approach  <cit> .
other approaches to this problem include the empirical bayesian  method  <cit>  and the significance analysis of microarray  method  <cit> .
the multiplicity problem is addressed in adopting a resampling-based approach to controlling fdr  <cit> .
also an anova formulation and an empirical bayes adjustment to the t-statistics  <cit>  and an empirical bayes screening procedure have been proposed  <cit> .
there has been considerable research about discovering patterns using clustering and testing including clustering after transformation and smoothing as a technique for nonparametrically estimating and clustering a large number of curves  <cit>  and clustering short time series gene expression data by selecting a set of potential expression profiles  <cit> .
smoothing away noise-induced wiggles of gene expression data with fourier series for microarray data has been considered including an improved fourier method with irregular or monotonic components of cell-cycle expression  <cit> , a two-step procedure for clustering periodic patterns of gene expression profiles using a fourier series approximation with frequency and amplitude of order one  <cit> , a multivariate modeling approach using partial least squares  regression to identify genes with periodic fluctuations in the budding yeast cell cycle data  <cit> , a hidden markov models  approach to account for the horizontal dependencies along the time axis  <cit> , and a model-based clustering of the fourier coefficients calculated on the first difference of the time-course data  <cit> .
model-based hierarchical clustering was proposed in character recognition problems using a multivariate normal model  <cit>  and it may be used to guide the choice of the model based on computing an approximate maximum for the classification likelihood  <cit> .
there has been much work done on clustering microarray data, mostly on grouping common expression patterns.
however, less attention has been paid to time-course gene studies.
currently the analysis of gets  is commonly performed using a gp   <cit> .
also a bayesian analysis of microarray time series has been developed with the software package bats  <cit> .
in this research, we propose a new method for gene screening using fourier coefficients to cluster time-courses of genes that exhibit similar patterns.
this paper introduces a methodology for gene selection based on time-course data.
the first step is screening, in which we seek to isolate the inactive genes from the active ones, while properly taking into account the serial dependence in the time course data and controlling the fdr, all in the fourier domain.
the second step involves a model-based clustering of the “active” genes, also in the fourier domain.
we evaluate the performance of the methodology using both simulated data and yeast cell cycle data.
RESULTS
simulated data
since real expression data sets are generally noisy and their clusters may not be fully reflective of the class information, we first evaluate the performance of our method with simulated data, for which the “true” classes are known.
we simulate data according to the regression model
yiu=fitiu+ϵiui= <dig> ,···n,u= <dig> ,···,m
where n =  <dig> genes, m =  <dig> time points, and e =  <dig> and ϵiu’s from an autoregressive ar process with a variety of values of the ar parameter.
the regression functions for f are:
f1t= <dig>
f2t=10t
f3t=min2−5t <dig> t−232+sin5πt <dig>
f4t=−f3t
f5t=2cos2πt
f6t=5+f5t
each simulated dataset consists of  <dig> curves originating from the  <dig> functions:  <dig> f <dig>  s and  <dig> curves of each f <dig>  ⋯, f <dig>  to reflect typical gene expression data.
thus, there are  <dig> sets of differential genes and  <dig> set of non-differential genes.
the standard deviation of the innovation process was set to σ =  <dig>  and σ =  <dig>  to represent low and high noise situations, respectively.
the cosine system 2cos is used as the set of basis functions.
though the optimal choice for j could vary from function to function, we choose to use a single smoothing parameter that performs reasonably well for all of the curves.
in the simulation ten fourier coefficients are used for the spectrum estimation.
several numbers of fourier coefficients are considered for test statistics in the proposed screening method.
the number of clusters is determined according to the bayesian information criterion .
let t be a clustering map defined as
tf,g= <dig> ,iffandgareinthesameclusterotherwise.
regarding the estimation error, the clustering estimation error rate η depending on k clusters is defined as
ηk=2nn−1∑r<si≠t^k)
where {f <dig>  ⋯, fn} denote the true curves and f^ <dig> ⋯,f^n denote the estimated curves.
let t and t^ represent the corresponding cluster maps, and k denote the number of clusters.
n is the fraction of all pairs that are incorrectly placed in different clusters.
we compare our screening method with the recently proposed gpr  screening  <cit> .
gpr seeks to quantify the true signal and noise in a gene expression time series, allows us to rank the differential expression of the gene profile.
a gaussian process using a squared-exponential covariance function is based on the assumption that the underlying true signal in a profile is a smooth function.
gpr is applied to each gene curve with the assumption that each gene can be categorized as either quiet or differentially expressed.
the genes may then be ranked in decreasing order according to their values of likelihood ratio  test statistics for testing between these two characterizations.
the optimal critical value for the lr test statistics for gpr screening was empirically determined to be log based on the true positive rate  since in the simulation, this cutoff allowed more than 80% of differentially expressed genes to be detected.
there is no clear-cut critical value for this scheme.
the genes greater than the critical value are detected as differential.
after the differential genes are obtained with gpr screening, clustering procedure can be done with those genes.
to summarize the performance across the  <dig> replications of  <dig> curves in each data set, we compute four performance measures to evaluate the procedures:
i. sensitivity: proportion of differentially expressed genes that are declared significant
ii.
specificity: proportion of non-differentially expressed genes that are not declared significant
iii.
false discovery rate : proportion of genes declared significant that are not differentially expressed
iv.
false non-discovery rate : proportion of genes not declared significant that are differentially expressed
tables  <dig> and  <dig> show the clustering estimation error rates, average silhouette values and adjusted rand index values  for the model-based clustering without screening versus with the proposed screening according to the positive correlation.
they also show the sensitivity, specificity, fdr and fnr of our proposed screening procedure and gpr screening.
* fc: proposed method with fourier coefficients, **gpr: gaussian process regression.
comparison of estimation error rate , silhouette width  and adjusted rand index  values of model-based clustering without screening vs with screening with j fourier coefficients including sensitivity, specificity, fdr and fnr with m =  <dig> time points.
these summaries are based on  <dig> repetitions of each consisting of  <dig> curves with ar parameter ρ’s with the noise standard deviation σ =  <dig> .
* fc: proposed method with fourier coefficients, **gpr: gaussian process regression
comparison of estimation error rate , silhouette width  and adjusted rand index  values of model-based clustering without screening vs with screening with j fourier coefficients including sensitivity, specificity, fdr and fnr with m =  <dig> time points.
these summaries are based on  <dig> repetitions of each consisting of  <dig> curves with ar parameter ρ s with the noise standard deviation σ =  <dig> .
as shown in table  <dig> the error rates of the high noise case are bigger and the sensitivity is smaller than those of the lower noise case in table  <dig>  however the high noise level does not diminish the performance of the screening procedure.
from tables  <dig> and  <dig> it can be seen that the clustering estimation error is smaller after screening than it is without screening.
also, the clustering estimation error becomes smaller as the number of fourier coefficients j becomes larger and for smaller values of the ar parameter.
table  <dig>  shows that the screening percentage of our method is a little higher than gpr for some choices of j. overall, the proposed method demonstrates improved sensitivity according to the number of fourier coefficients j and much improved specificity and fdr as compared to gpr.
in addition, the proposed method has an advantage that it does not require estimation of the covariance structure
yeast cell cycle data analysis
we have used alpha synchronized yeast cell expression data  <cit>  available at http://genome-www.stanford.edu/cellcycle/ to test our algorithm.
after removing genes with missing values, there were  <dig>  genes remaining out of  <dig> genes.
this data contained  <dig> time points sampled uniformly every 7 min between  <dig> and 119 min.
following  <cit> , we assumed a first-order auto-correlation structure for the error terms.
the method was repeated for each of several choices for j. table  <dig> shows the median and the average silhouette values with euclidean distance between samples by model-based clusterings for various j values both with and without the screening step using a significance level of fdr 5%.
the number of genes with differentially expression is  <dig>  out of  <dig>  at the significance level α =  <dig> .
median and average silhouette values for model-based clustering with fourier coefficients using euclidean distance with screening vs. without screening.
judging from the silhouette value, the model-based with  <dig> fourier coefficients and  <dig> clusters was considered most appropriate.
therefore it should be noted that silhouette values of euclidean distance between two clustering models may not be the only criterion for model comparison.
rather, as in the following gene ontology analysis, clustering should be evaluated based on biological interpretation of results.
with j =  <dig>  the model-based clustering approach results in  <dig> clusters consisting of  <dig>   <dig>   <dig>  and  <dig> genes, respectively.
figure  <dig> shows plots of the sample fourier coefficients.
figure  <dig> shows pointwise means of fourier estimated gene scores in each cluster with j =  <dig> sample fourier coefficients.
the graph in the bottom left-hand corner of figure  <dig> shows the estimated mean of gene scores of screened out.
gaussian mixture model clustering allows clusters to have different orientation or sizes while preserving some common features, such as an ellipsoidal shape.
clusters  <dig>   <dig> and  <dig> in particular show a cycle while cluster  <dig> consists of less active genes.
we also applied gpr screening for yeast data with the critical value log  and identified  <dig>  non-quiet differentially expressed genes.
a gaussian mixture model clustering algorithm was applied to these genes indicating  <dig> clusters.
the clusters have  <dig>   <dig>   <dig>  and  <dig> genes, respectively.
for this clustering the median silhouette value is  <dig>  and the average silhouette value is  <dig> , each less than the corresponding silhouette summaries for the proposed procedure.
owing to noise and the high dimensionality of data, careful consideration of statistical and biological validity is needed when analyzing microarray data.
from our review we have found that without plausible interpretation and biological validation, the number of partitions produced by numerical analysis is highly unreliable, and sometimes even misleading.
in order to evaluate our clustering analysis, gene ontology  is applied to the clustered genes  <cit> .
go consists of three organizing principles: biological processes, molecular functions, and cellular components.
biological process evidences will be used in this study because the yeast dataset was obtained from the cell cycle process.
the go database provides useful tools to annotate and analyze a set of genes.
for example, gostat searches for statistically overrepresented go annotations by evaluating the significance of functional processes and molecular mechanisms  <cit> .
this tool simply derives the statistical significance between expected and observed functional categories based on the fisher’s exact test.
so we firstly apply this tool to our four clusters and select significantly overrepresented go terms in each cluster with a criterion p-value <  <dig> .
along with the four clusters, we also look for the significant go terms of the screened  <dig>  genes for the comparison.
before performing the hypergeometric tests, we filtered out the genes which cannot be identified from the yeast annotation database .
table  <dig> shows the number of genes in each cluster before and after the filtering and the selected  go terms from the hypergeometric test of the clustered genes.
the number of genes screened, screened out and significant genes with respect to go.
even though the number of genes affects to the hypergeometric test, cluster  <dig> and the screened-out group have only one and six significantly overrepresented go terms, respectively.
this means that all the genes  in those clusters rarely share their biological processes and these clusters can be considered as random collections of genes.
so, we focused on the three clusters  <dig>   <dig>  and  <dig> to find their biological meanings.
in order to identify the relationships among the selected go terms, we construct a go graph of each cluster.
this graph is constructed by locating the selected terms as leaf nodes and linking all the nodes to their ancestors until their root term.
note that whatever go terms are selected in a cluster, the cluster has only one go relationship graph because every go terms are eventually ended up at the root term if we follow their ancestors.
figure  <dig> depicts the go graphs of the three clusters.
gray colored nodes represent selected go terms in each cluster.
we realize that most of the selected go terms are related with each other as a parent–child relationship and they tend to be closely located in each graph.
among the selected go terms, we looked into the terms which are connected sequentially from the top node to the bottom .
this cascade form of go terms provides more enhanced evidences that the corresponding genes are more closely related in their biological processes than that of a parent–child relationship.
these sequentially connected terms are labeled by their subset number in the figure  <dig> and are summarized in table  <dig>  in cluster  <dig>  subset  <dig> includes the genes mainly affect to cell cycle especially mitosis.
mitosis is a division process that produces two daughter cells having the same genetic information as their parent cell.
during this mitosis, structural assembly of dna and nucleosome is processed, which can be represented in the subset  <dig> of cluster  <dig>  mitosis is followed by cytokinesis and the cell wall of the daughter cells is formed, whose related genes are shown in cluster  <dig>  in cluster  <dig>  genes in subset  <dig> are in charge of dna replication in the s phase of cell cycle.
so, our method enables us to identify the genes that are expressed in dynamical cellular events of dna duplication and cell division.
though the subset  <dig> and  <dig> of cluster  <dig> seem to be more related with the responses to dna stresses then cell cycle, it is known that heat shock proteins are also responsible for cell proliferation and cell cycle .
therefore, based on this result, further experimental investigation could be possible to reveal the link between two different biological processes, “heat-shock response” and “cell cycle”.
cluster  <dig>   <dig> and  <dig> have biologically meaningful genes as shown in the table.
CONCLUSIONS
a number of recent studies in this field have focused on the analysis of time series of gene expression data, collected by performing dna microarray experiments at several or more points in time.
we have proposed a significance method to identify differentially expressed genes in time course microarray gene expression data using time series screening based on fourier coefficients controlling fdr and model based clustering with the sample genewise fourier coefficients, and have compared our screening method with gp screening.
recently spectral mixture kernels  <cit>  have been introduced with a gaussian mixture as a fourier transform of kernels and these kernels are able to discover patterns and extrapolate and model negative covariances, illustrating the relationship between the gp and the fourier approach.
we demonstrated the effectiveness of our approach using model-based clustering of gene profiles.
although we assumed that the residuals follow an ar process, we found that it is not necessary to assume a specific correlation structure since the sample fourier coefficient estimates themselves do not depend heavily on the underlying covariance structure.
the most commonly used techniques are clustering  techniques, which are particularly well suited for an exploratory investigation of this kind of data.
the main advantage of the model-based methods is their reliance on a highly structured theoretical basis.
model-based clustering methods are based on the assumption that the data were generated by some underlying model and attempt to infer these models from data.
data generated by the same model is then considered to be “similar” and clustered together.
also, the choice of the optimal number of clusters and the selection of the best model can be performed using sound statistical criteria.
the proposed method is able to identify a set of cell-cycle-regulated genes in yeast and time-course genes.
the proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics.

 time-course gene expression data are often measured to study dynamic biological systems and gene regulatory networks. array technologies have made it straightforward to monitor the expression pattern of thousands of genes simultaneously. the challenge now is to interpret such massive data sets. the first step is to extract the fundamental patterns of gene expression inherent in the data. gene-expression levels can be monitored with cdna or oligonucleotide chips over a time-course for a temporal process. following a microarray time series experiment, a key challenge is to extract the continuous representation of all genes throughout the time-course. identifying significant or differentially expressed genes is challenging because different genes may have different profiles, and because of the noise present in time series expression data. a comprehensive review about time series expression data analysis and the related computational challenges may be found in. microarrays have recently been used for the purpose of monitoring expression levels of thousands of genes simultaneously and for identifying genes that are differentially expressed. with the number of inferences made in the analysis of microarray data, it is natural to be concerned about multiple testing. this problem of multiplicity can be dealt with by controlling the false discovery rate. in the past decade, many approaches to gene selection have been considered including a two sample t-test, a regression approach, and a mixture model approach. other approaches to this problem include the empirical bayesian method and the significance analysis of microarray method. the multiplicity problem is addressed in adopting a resampling-based approach to controlling fdr. also an anova formulation and an empirical bayes adjustment to the t-statistics and an empirical bayes screening procedure have been proposed. there has been considerable research about discovering patterns using clustering and testing including clustering after transformation and smoothing as a technique for nonparametrically estimating and clustering a large number of curves and clustering short time series gene expression data by selecting a set of potential expression profiles. smoothing away noise-induced wiggles of gene expression data with fourier series for microarray data has been considered including an improved fourier method with irregular or monotonic components of cell-cycle expression, a two-step procedure for clustering periodic patterns of gene expression profiles using a fourier series approximation with frequency and amplitude of order one, a multivariate modeling approach using partial least squares regression to identify genes with periodic fluctuations in the budding yeast cell cycle data, a hidden markov models approach to account for the horizontal dependencies along the time axis, and a model-based clustering of the fourier coefficients calculated on the first difference of the time-course data. model-based hierarchical clustering was proposed in character recognition problems using a multivariate normal model and it may be used to guide the choice of the model based on computing an approximate maximum for the classification likelihood. there has been much work done on clustering microarray data, mostly on grouping common expression patterns. however, less attention has been paid to time-course gene studies. currently the analysis of gets is commonly performed using a gp. also a bayesian analysis of microarray time series has been developed with the software package bats. in this research, we propose a new method for gene screening using fourier coefficients to cluster time-courses of genes that exhibit similar patterns. this paper introduces a methodology for gene selection based on time-course data. the first step is screening, in which we seek to isolate the inactive genes from the active ones, while properly taking into account the serial dependence in the time course data and controlling the fdr, all in the fourier domain. the second step involves a model-based clustering of the “active” genes, also in the fourier domain. we evaluate the performance of the methodology using both simulated data and yeast cell cycle data.  simulated data since real expression data sets are generally noisy and their clusters may not be fully reflective of the class information, we first evaluate the performance of our method with simulated data, for which the “true” classes are known. we simulate data according to the regression model yiu=fitiu+ϵiui=,···n,u=,···,m where n =  genes, m =  time points, and e =  and ϵiu’s from an autoregressive ar process with a variety of values of the ar parameter. the regression functions for f are: f1t= f2t=10t f3t=min2−5t t−232+sin5πt f4t=−f3t f5t=2cos2πt f6t=5+f5t each simulated dataset consists of curves originating from the functions: f s and curves of each f  ⋯, f to reflect typical gene expression data. thus, there are sets of differential genes and set of non-differential genes. the standard deviation of the innovation process was set to σ =  and σ =  to represent low and high noise situations, respectively. the cosine system 2cos is used as the set of basis functions. though the optimal choice for j could vary from function to function, we choose to use a single smoothing parameter that performs reasonably well for all of the curves. in the simulation ten fourier coefficients are used for the spectrum estimation. several numbers of fourier coefficients are considered for test statistics in the proposed screening method. the number of clusters is determined according to the bayesian information criterion. let t be a clustering map defined as tf,g=,iffandgareinthesameclusterotherwise. regarding the estimation error, the clustering estimation error rate η depending on k clusters is defined as ηk=2nn−1∑r<si≠t^k) where {f  ⋯, fn} denote the true curves and f^ ⋯,f^n denote the estimated curves. let t and t^ represent the corresponding cluster maps, and k denote the number of clusters. n is the fraction of all pairs that are incorrectly placed in different clusters. we compare our screening method with the recently proposed gpr screening. gpr seeks to quantify the true signal and noise in a gene expression time series, allows us to rank the differential expression of the gene profile. a gaussian process using a squared-exponential covariance function is based on the assumption that the underlying true signal in a profile is a smooth function. gpr is applied to each gene curve with the assumption that each gene can be categorized as either quiet or differentially expressed. the genes may then be ranked in decreasing order according to their values of likelihood ratio test statistics for testing between these two characterizations. the optimal critical value for the lr test statistics for gpr screening was empirically determined to be log based on the true positive rate since in the simulation, this cutoff allowed more than 80% of differentially expressed genes to be detected. there is no clear-cut critical value for this scheme. the genes greater than the critical value are detected as differential. after the differential genes are obtained with gpr screening, clustering procedure can be done with those genes. to summarize the performance across the replications of curves in each data set, we compute four performance measures to evaluate the procedures: i. sensitivity: proportion of differentially expressed genes that are declared significant ii. specificity: proportion of non-differentially expressed genes that are not declared significant iii. false discovery rate: proportion of genes declared significant that are not differentially expressed iv. false non-discovery rate: proportion of genes not declared significant that are differentially expressed tables  and show the clustering estimation error rates, average silhouette values and adjusted rand index values for the model-based clustering without screening versus with the proposed screening according to the positive correlation. they also show the sensitivity, specificity, fdr and fnr of our proposed screening procedure and gpr screening. * fc: proposed method with fourier coefficients, **gpr: gaussian process regression. comparison of estimation error rate, silhouette width and adjusted rand index values of model-based clustering without screening vs with screening with j fourier coefficients including sensitivity, specificity, fdr and fnr with m =  time points. these summaries are based on repetitions of each consisting of curves with ar parameter ρ’s with the noise standard deviation σ = . * fc: proposed method with fourier coefficients, **gpr: gaussian process regression comparison of estimation error rate, silhouette width and adjusted rand index values of model-based clustering without screening vs with screening with j fourier coefficients including sensitivity, specificity, fdr and fnr with m =  time points. these summaries are based on repetitions of each consisting of curves with ar parameter ρ s with the noise standard deviation σ = . as shown in table  the error rates of the high noise case are bigger and the sensitivity is smaller than those of the lower noise case in table  however the high noise level does not diminish the performance of the screening procedure. from tables  and it can be seen that the clustering estimation error is smaller after screening than it is without screening. also, the clustering estimation error becomes smaller as the number of fourier coefficients j becomes larger and for smaller values of the ar parameter. table  shows that the screening percentage of our method is a little higher than gpr for some choices of j. overall, the proposed method demonstrates improved sensitivity according to the number of fourier coefficients j and much improved specificity and fdr as compared to gpr. in addition, the proposed method has an advantage that it does not require estimation of the covariance structure yeast cell cycle data analysis we have used alpha synchronized yeast cell expression data available at http://genome-www.stanford.edu/cellcycle/ to test our algorithm. after removing genes with missing values, there were genes remaining out of genes. this data contained time points sampled uniformly every 7 min between and 119 min. following, we assumed a first-order auto-correlation structure for the error terms. the method was repeated for each of several choices for j. table  shows the median and the average silhouette values with euclidean distance between samples by model-based clusterings for various j values both with and without the screening step using a significance level of fdr 5%. the number of genes with differentially expression is out of at the significance level α =. median and average silhouette values for model-based clustering with fourier coefficients using euclidean distance with screening vs. without screening. judging from the silhouette value, the model-based with fourier coefficients and clusters was considered most appropriate. therefore it should be noted that silhouette values of euclidean distance between two clustering models may not be the only criterion for model comparison. rather, as in the following gene ontology analysis, clustering should be evaluated based on biological interpretation of results. with j =  the model-based clustering approach results in clusters consisting of and genes, respectively. figure  shows plots of the sample fourier coefficients. figure  shows pointwise means of fourier estimated gene scores in each cluster with j =  sample fourier coefficients. the graph in the bottom left-hand corner of figure  shows the estimated mean of gene scores of screened out. gaussian mixture model clustering allows clusters to have different orientation or sizes while preserving some common features, such as an ellipsoidal shape. clusters and in particular show a cycle while cluster consists of less active genes. we also applied gpr screening for yeast data with the critical value log and identified non-quiet differentially expressed genes. a gaussian mixture model clustering algorithm was applied to these genes indicating clusters. the clusters have and genes, respectively. for this clustering the median silhouette value is and the average silhouette value is, each less than the corresponding silhouette summaries for the proposed procedure. owing to noise and the high dimensionality of data, careful consideration of statistical and biological validity is needed when analyzing microarray data. from our review we have found that without plausible interpretation and biological validation, the number of partitions produced by numerical analysis is highly unreliable, and sometimes even misleading. in order to evaluate our clustering analysis, gene ontology is applied to the clustered genes. go consists of three organizing principles: biological processes, molecular functions, and cellular components. biological process evidences will be used in this study because the yeast dataset was obtained from the cell cycle process. the go database provides useful tools to annotate and analyze a set of genes. for example, gostat searches for statistically overrepresented go annotations by evaluating the significance of functional processes and molecular mechanisms. this tool simply derives the statistical significance between expected and observed functional categories based on the fisher’s exact test. so we firstly apply this tool to our four clusters and select significantly overrepresented go terms in each cluster with a criterion p-value <. along with the four clusters, we also look for the significant go terms of the screened genes for the comparison. before performing the hypergeometric tests, we filtered out the genes which cannot be identified from the yeast annotation database. table  shows the number of genes in each cluster before and after the filtering and the selected go terms from the hypergeometric test of the clustered genes. the number of genes screened, screened out and significant genes with respect to go. even though the number of genes affects to the hypergeometric test, cluster and the screened-out group have only one and six significantly overrepresented go terms, respectively. this means that all the genes in those clusters rarely share their biological processes and these clusters can be considered as random collections of genes. so, we focused on the three clusters and to find their biological meanings. in order to identify the relationships among the selected go terms, we construct a go graph of each cluster. this graph is constructed by locating the selected terms as leaf nodes and linking all the nodes to their ancestors until their root term. note that whatever go terms are selected in a cluster, the cluster has only one go relationship graph because every go terms are eventually ended up at the root term if we follow their ancestors. figure  depicts the go graphs of the three clusters. gray colored nodes represent selected go terms in each cluster. we realize that most of the selected go terms are related with each other as a parent–child relationship and they tend to be closely located in each graph. among the selected go terms, we looked into the terms which are connected sequentially from the top node to the bottom. this cascade form of go terms provides more enhanced evidences that the corresponding genes are more closely related in their biological processes than that of a parent–child relationship. these sequentially connected terms are labeled by their subset number in the figure  and are summarized in table  in cluster subset includes the genes mainly affect to cell cycle especially mitosis. mitosis is a division process that produces two daughter cells having the same genetic information as their parent cell. during this mitosis, structural assembly of dna and nucleosome is processed, which can be represented in the subset of cluster mitosis is followed by cytokinesis and the cell wall of the daughter cells is formed, whose related genes are shown in cluster in cluster genes in subset are in charge of dna replication in the s phase of cell cycle. so, our method enables us to identify the genes that are expressed in dynamical cellular events of dna duplication and cell division. though the subset and of cluster seem to be more related with the responses to dna stresses then cell cycle, it is known that heat shock proteins are also responsible for cell proliferation and cell cycle. therefore, based on this result, further experimental investigation could be possible to reveal the link between two different biological processes, “heat-shock response” and “cell cycle”. cluster and have biologically meaningful genes as shown in the table.  a number of recent studies in this field have focused on the analysis of time series of gene expression data, collected by performing dna microarray experiments at several or more points in time. we have proposed a significance method to identify differentially expressed genes in time course microarray gene expression data using time series screening based on fourier coefficients controlling fdr and model based clustering with the sample genewise fourier coefficients, and have compared our screening method with gp screening. recently spectral mixture kernels have been introduced with a gaussian mixture as a fourier transform of kernels and these kernels are able to discover patterns and extrapolate and model negative covariances, illustrating the relationship between the gp and the fourier approach. we demonstrated the effectiveness of our approach using model-based clustering of gene profiles. although we assumed that the residuals follow an ar process, we found that it is not necessary to assume a specific correlation structure since the sample fourier coefficient estimates themselves do not depend heavily on the underlying covariance structure. the most commonly used techniques are clustering techniques, which are particularly well suited for an exploratory investigation of this kind of data. the main advantage of the model-based methods is their reliance on a highly structured theoretical basis. model-based clustering methods are based on the assumption that the data were generated by some underlying model and attempt to infer these models from data. data generated by the same model is then considered to be “similar” and clustered together. also, the choice of the optimal number of clusters and the selection of the best model can be performed using sound statistical criteria. the proposed method is able to identify a set of cell-cycle-regulated genes in yeast and time-course genes. the proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics. 
the proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics. this work aims to identify genes that show different gene expression profiles across time. finally, we cluster the remaining gene profiles using a model-based approach in the fourier domain. the key elements of the proposed methodology: representation of gene profiles in the fourier domain; automatic screening of genes based on the fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate; model-based clustering of the remaining gene profiles. we evaluate the screening results in terms of sensitivity, specificity, fdr and fnr, compare with the gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization. time course gene expression experiments are an increasingly popular method for exploring biological processes. since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. in particular, we first represent each profile in terms of a fourier basis, and then we screen out genes that are not differentially expressed based on the fourier coefficients.
 time course gene expression experiments are an increasingly popular method for exploring biological processes. temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. with such data it is possible to study gene expression changes over time and thereby to detect differential genes. much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis.  this work aims to identify genes that show different gene expression profiles across time. we propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. in particular, we first represent each profile in terms of a fourier basis, and then we screen out genes that are not differentially expressed based on the fourier coefficients. finally, we cluster the remaining gene profiles using a model-based approach in the fourier domain. we evaluate the screening results in terms of sensitivity, specificity, fdr and fnr, compare with the gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization. the key elements of the proposed methodology: representation of gene profiles in the fourier domain; automatic screening of genes based on the fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate; model-based clustering of the remaining gene profiles.  using this method, we identified a set of cell-cycle-regulated time-course yeast genes. the proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics. 