Missing Value Estimation In Microarray Data Using

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For a number of reasons, microarray data sets frequently contain some missing values ... Therefore missing value estimation is essential as a preprocessing step to ... objects containing missing values [4], that usually loses too much useful ...

P a g e |18 Vol. 10 Issue 12 (Ver. 1.0) October 2010

Global Journal of Computer Science and Technology

Missing Value Estimation In Microarray Data Using Fuzzy Clustering And Semantic Similarity Mohammad Mehdi Pourhashem1, Manouchehr Kelarestaghi2, Mir Mohsen Pedram3 Abstract-Gene expression profiling plays an important role in a broad range of areas in biology. Microarray data often contains multiple missing expression values, which can significantly affect subsequent analysis In this paper, a new method based on fuzzy clustering and genes semantic similarity is proposed to estimate missing values in microarray data. In the proposed method, microarray data are clustered based on genes semantic similarity and their expression values and missing values are imputed with values generated from cluster centers Genes similarity in clustering process determine with their semantic similarity obtained from gene ontology as well as their expression values. The experimental results indicate that the proposed method outperforms other methods in terms of Root Mean Square error.

Keywords-microarray, missing value estimation, fuzzy clustering, semantic similarity




icroarray is a technology for the monitoring of thousands of gene expression levels simultaneously [1]. Data from microarray experiments are usually in the form of large matrices of expression levels of genes (rows) under different experimental conditions (columns). For a number of reasons, microarray data sets frequently contain some missing values; typical reasons include insufficient resolution, image corruption, spotting or scratches on the slide, dust or hybridization failures [2]. Therefore missing value estimation is essential as a preprocessing step to obtain proper results from microarray data analysis. There are several approaches to deal with missing values. The first approach is repeating the experiment [3], which is expensive and time consuming. The second approach is ignoring objects containing missing values [4], that usually loses too much useful information and may bias the results if the remaining cases are unrepresentative of the entire sample.The third approach is estimating the missing values, which can be subdivided into two groups. The first group doesn‘t consider the correlation structure among the genes. These methods substitute the missing values by a global constant such as 0 [4], or by the average of the available values for that gene [5]. Both of these methods distort relationships among variables. The second groups consider the correlation structure. In fact the estimating procedure consists of two steps: in the first step similar genes to the _________________________ About1- Computer Engineering Department, Islamic Azad University-Arak Branch, Arak, Iran,[email protected] About2- Computer Engineering Department, Tarbiat Moallem University, Karaj/ Tehran, Iran,[email protected] About3- Computer Engineering Department, Tarbiat Moallem University, Karaj/ Tehran, Iran,[email protected]

GJCST Classification (FOR) H.3.3, I.5.3

gene with missing value, are selected and in the second step the missing values are predicted using observed values of selected genes, for example the widely used weighted Knearest neighbor imputation (KNNimpute), reconstructs the missing values using a weighted average of K most similar genes [6]. These methods have better performance than simple methods such as substituting missing values by a constant or by row average, but their drawback is that estimation ability of them depends on K parameter (number of gene neighbor used to estimate missing value). There is no theoretical way, however, to determine this parameter appropriately and should be specified by user. In [2, 7] cluster-based algorithms have been proposed to deal with missing values which don‘t need user to determine parameters [8].A limitation of the methods mentioned above, is that they use no external information but the estimation is based solely on the expression data. In [8] a method based on Fuzzy C-means clustering algorithm (FCM) and gene ontology have been proposed to avoid the problems of those methods. This method (FCMGOimpute) uses information of gene ontology as external information, furthermore microarray data. There‘s a prospect that similar genes have close expression levels. In FCMGOimpute method two genes will be similar if they have the same annotations. This similarity measure is not good enough.In this paper, we propose a new missing value estimation method based on Fuzzy C-means clustering algorithm (FCM) and genes semantic similarity to avoid the problems of previous methods and be more accurate in evaluate genes similarity.The structure of this paper is as follows: Section 2 describes FCMGOimpute method and the proposed method to enhance it. In Section 3, the experimental results are shown, and finally some discussions are given in Section 4. II.


The clustering aim is to decompose a given set of objects into subgroups or clusters based on similarity. Whereas each gene may be involved in more than one biological process, hard clustering methods which assign each gene to only one cluster can not ensure this characteristic of the genes [9]. We expect that single genes may belong to several clusters, and the clustering algorithm should handle incomplete data. With these requirements, FCM algorithm in [2] is a proper clustering algorithm. In the clustering process, we have used gene ontology annotation as external information to determine the semantic similarity of genes and acquire more biologically interpretable clusters.

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This method uses FCM clustering for cluster microarray data that is an incomplete data. Fuzzy clustering method allows one object to belong to several clusters. Each object belongs to a cluster with a membership degree between 0 and 1 [10].The data from microarray experiments is usually in the form of large matrices of expression levels of genes (rows) under different experimental conditions (columns). This matrix calledG and a matrix Ehas been defined, where Eki is equal to 0, if corresponding component in G (Gki) is a missing value and equal to 1 otherwise. Let be the set of given genes of matrix G (gi is i‘th row of matrix G) and let c be the number of clusters. Then membership degree of data object gk to cluster i is defined as uik, which holds the below constraints:

Fuzzy C-means clustering is based on minimization of the following objective function:

where m is fuzziness parameter which is a real number greater than 1, and dik2 is the Euclidean distance between data object gk and cluster center i which is defined by:

where s is the feature space dimension, and Bkt is defined based on gene ontology annotations of gene k and gene t, as follows: (5)

Therefore, the annotation of gk is compared with annotation of all genes belonging to cluster i, more genes have the same annotation, more the distance shrink. Of course not all the genes have the same effects, therefore we multiply Bkt to the membership degree of gene gt to cluster i; Consequently the genes which belong to cluster i with higher membership degree, have more effect [8].In case the gk is an unknown gene, Bkt is equal to 0 for all t (1 ≤ t ≤ N ), and consequently the second term of equation (4) is equal to 1 [8]. It leads to Euclidean distance which only consider gene expression levels and used in FCMimpute method.The algorithm minimizes the objective function shown in (3), by updating of the cluster centers and membership degrees, iteratively by Equation (6) and (7).

To determine the fuzziness parameter (m) and the number of clusters (c), some methods were proposed in [2]. 2)

Improving Similarity Criterion In FCMGOimpute By Using Genes Semantic Similarity

In FCMGOimpute two genes are similar, if they have same annotation, and they are dissimilar if theirannotations are different. According to this definition, similarity value will be 0 or 1. Since, similarity concept isn‘t crisp;we use semantic similarity as similarity criterion between genes,which will be a real value between 0 and 1.For example and further explain, suppose we have two genes that all of their annotation terms are equal except one. Based on similarity criterion in FCMGOimpute these genes are dissimilar and similarity measure will be 0, but their semantic similarity may be 0.9. While, similarity measure between these two genes must affect the clustering and estimation process by value of 0.9, not 0 To measure the semantic similarity between two genes, the first step is to establish the semantic similarity between their annotated GO terms in the ontology. One of the most widely used approaches is based on the information theory. Given a term t, the occurrence of t, occur(t) is defined as the number of times t occurs in the annotation database being analyzed. The frequency of the term t, freq(t) is the summation of occurrence of t and all its descendantsdefined as,

where ancestors(ti) is the set of ti‘s ancestors. This definition is based on the fact that if a gene product is annotated by a term, then it is also annotated by its parent terms. Therefore, given any term, we can estimate its probability of being directly or indirectly annotated by gene products in a corpus, which is defined as [11],

where troot is the root term of the ontology that t belongs to. In GO, troot could be Molecular Function (MF), Cellular Component (CC), or Biological Process (BP). Obviously, p(MF) = p(CC) = p(BP) = 1. Now, the information content of term t, IC(t) can be define as: Given a pair of terms, tiand tj, their shared information content is defined as [11]: where S(ti,tj) = ancestors(ti)∩ancestors(tj). Since IC(t)≥IC(ancestors(t)), the maximum information content of their common ancestors should be the information carried by their least common ancestor [11].We will use Lin term semantic similarity [12] that is defined as:

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We will use gene semantic similarity as: [11]

We modify the calculation of Euclidean distance in (4) as follows:

Calculation of cluster centers and membership degree is the same as (6) and (7). 3)

Imputation of missing values

We utilize the clustering results to estimate the imputation of missing values in microarray data set. We impute missing values by making use of the weighted mean of the values of the corresponding attribute over all clusters. The weighting factors are the membership degrees uik of a gene gk to the cluster ci. The missing gene expression value gkj is imputed by:



We compared our proposed method (FCMSSimpute) with the previously developed FCMimpute and FCMGOimpute methods by imputation of microarray data. Data set used in this work was selected from publically available microarray data. Five microarray were used: two microarray of yeast cells response to environmental changes, data A [13] and B [14], three microarray are time series of yeast, data C, D and E [15]. We collected GO annotation for the genes in thisdata set from [16] and necessary terms semantic similarity for compute genes semantic similarity from [17].Before applying the imputation algorithms, each data set was preprocessed for the evaluation by removing rows containing missing expression values, yielding ‗complete‘ matrices. Between 1% and 20% of the data weredeleted at random to create test data sets. Each method was then usedto recover the introduced missing valuesfor each data set, and the estimated values were compared to those in the original data set. To compare the accuracy of different imputation methods, we used RMSE (Root Mean Squared Error) as evaluation metric:

Global Journal of Computer Science and Technology

Global Journal of Computer Science and Technology

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Figure 1. Comparison of the accuracy of FCMSSimpute, FCMGOimpute and FCMimpute methods for five data set over 1% and 20% data missing. The accuracies were evaluated by RMSE.

where, R is the real value, I is the imputed value, and n is the number of missing values.The FCMimpute considers the correlation structure amongst the genes, but doesn‘t use any useful external information such as gene ontology, and uses just microarray data for imputation process. As it can be seen from the results, the FCMimpute has a lower performance, compared to other methods. FCMGOimpute has better performance over FCMimpute because it uses gene ontology annotation as anexternal information.As it is clearly observed from the Figure 1, the proposed method (FCMSSimpute) outperforms others in terms of accuracy. The proposed method considers the correlation structure amongst the genes. Additionally, it uses gene ontology annotation as an external information, and genes semantic similarity to measure genes similarity, which is more accurate from what defined in FCMGOimpute. Therefore the accuracy of imputation based on a well defined similarity of genes, will increase. IV.


In this paper, we proposed a new and efficient method for estimating missing values in microarray data, based on the using of genes semantic similarity. We take advantage of the correlation structure of the data to estimate missing expression values by clustering, as well as using genes semantic similarity which improves the imputation accuracy.We have analyzed the performance of our method on fivemicroarray and compared the accuracy with FCMimpute and FCMGOimpute methods. We observed that our method outperforms other methods in terms of the RMSE.In this paper, we have used weighted majority vote to determine the similarity of a gene to a cluster. We have used semantic similarity for measure similarity between genes. To compute semantic similarity, we have used molecular function annotation of genes, but there exist alternatives to define semantic similarity by use other term semantic similarity measures. Also Biological Process annotations can be used in similarity computation.


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P a g e |22 Vol. 10 Issue 12 (Ver. 1.0) October 2010 14) http://titan.biotec.uiuc.edu/rox1/download.html, 28 June 2010 15) http://www-genome.stanford.edu/mec1/data.shtml 28 june 2010 16) Saccharomyces Genome Database, http://db.yeastgenome.org/cgi-bin/batchDownload, 20 June 2010. 17) http://bioinformatics.clemson.edu/GSESAME/Program/GOCompareMultiple1.php.

Global Journal of Computer Science and Technology

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