- Proceedings
- Open Access
Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data
- Mi Hyeon Kim^{1},
- Hwa Jeong Seo^{2},
- Je-Gun Joung^{1, 3} and
- Ju Han Kim^{1}Email author
https://doi.org/10.1186/1471-2105-12-S13-S8
© Kim et al; licensee BioMed Central Ltd. 2011
- Published: 30 November 2011
Abstract
Background
Clustering-based methods on gene-expression analysis have been shown to be useful in biomedical applications such as cancer subtype discovery. Among them, Matrix factorization (MF) is advantageous for clustering gene expression patterns from DNA microarray experiments, as it efficiently reduces the dimension of gene expression data. Although several MF methods have been proposed for clustering gene expression patterns, a systematic evaluation has not been reported yet.
Results
Here we evaluated the clustering performance of orthogonal and non-orthogonal MFs by a total of nine measurements for performance in four gene expression datasets and one well-known dataset for clustering. Specifically, we employed a non-orthogonal MF algorithm, BSNMF (Bi-directional Sparse Non-negative Matrix Factorization), that applies bi-directional sparseness constraints superimposed on non-negative constraints, comprising a few dominantly co-expressed genes and samples together. Non-orthogonal MFs tended to show better clustering-quality and prediction-accuracy indices than orthogonal MFs as well as a traditional method, K-means. Moreover, BSNMF showed improved performance in these measurements. Non-orthogonal MFs including BSNMF showed also good performance in the functional enrichment test using Gene Ontology terms and biological pathways.
Conclusions
In conclusion, the clustering performance of orthogonal and non-orthogonal MFs was appropriately evaluated for clustering microarray data by comprehensive measurements. This study showed that non-orthogonal MFs have better performance than orthogonal MFs and K-means for clustering microarray data.
Keywords
- Gene Ontology
- Acute Lymphoblastic Leukemia
- Singular Value Decomposition
- Independent Component Analysis
- Acute Myelogenous Leukemia
Background
DNA microarray can simultaneously measure the expression levels of thousands of genes. Increasingly, the challenge is to interpret such data to reveal molecular biological processes and the mechanism of human diseases. One of the main goals of expression data analysis is to identify the changing and unchanging genes and to correlate these changes with similar expression profiles. One of the major challenges for gene expression analysis is the reduction of dimension. Gene expression data typically have high dimensionality, with tens of thousands of genes whereas the number of observations or experiments is usually under a hundred. Because the number of variables easily exceeds that of experiments, dimension reduction is obviously required for gene expression analysis. This task can be considered as a matrix factorization problem.
Matrix factorization (MF) methods on microarray data can extract distinct patterns from the data [1–5]. Principal Component Analysis (PCA) and Singular Value Decomposition (SVD) are popular analysis methods, and they have been applied to classification problems with satisfactory results [1, 5]. However, because of the holistic nature of PCA or SVD, it is difficult to provide the biologically instinctive interpretation of data from the obtained components. In order to overcome this limitation, Paatero and Tapper [6] and Lee and Seung [7] proposed that non-negative matrix factorization (NMF) can learn part-based representations that can provide the obvious interpretation. The non-negativity constraints make the representation purely additive (allowing no subtractions), in comparison with many other linear representations such as PCA and Independent Component Analysis (ICA) [8]. Their work was applied to signal processing and text mining. Brunet et al. [9] applied NMF to describe the gene expression profiles of all genes in terms of a few number of metagenes in order to derive meaningful biological information from cancer expression datasets. They clustered the samples into distinct subtypes by metagene expression patterns.
The gene expression patterns can be sparsely encoded by metagenes, implying a few significantly co-expressed genes. Several groups have proposed NMF formulation that enforces the sparseness of the decomposition. Li et al. [10] proposed local NMF (LNMF) that has additional constraints to enforce the sparseness in the NMF. Hoyer [11, 12] also proposed NMF formulation that can find parts-based representations by explicitly incorporating the concept of sparseness. Wang et al. [13] demonstrated Fisher non-negative matrix factorization (FNMF) that learns localized features by imposing Fisher constraints. Gao and Church [14] attempted to control sparseness by penalizing the number of non-zero entries unlike other methods.
Sample-based clustering, however, is not the only concern in microarray data analysis. Gene-based clustering provides informative sets of tightly co-regulated genes. While sample-based clustering relies on metagenes, gene-based clustering relies on meta-samples. The two processes can be viewed as bi-directionally constrained with each other. Good metagene may support good sample-based clusters and vice versa. Optimizing sample- dimension only, sparseness of gene-dimension is relatively decreased when sparseness of sample-dimension is increased. In result, the minimization problem is convex that was subsequently described by others [11, 12, 14, 15] and resulting matrix cannot support gene-based clusters well. Therefore, optimizing both sample and gene dimension together may be appropriated for clustering of microarray data. Here, we employed a novel non-orthogonal MF algorithm, Bi-directional Non-negative Matrix Factorization (BSNMF), with bi-directional sparseness constraints superimposed on non-negative constraints, comprising a few dominantly co-expressed genes and samples together. The bi-directional optimization process may provide quality clustering with improved biological relevance that may not be achieved by applying MFs for each dimension separately.
Many clustering-based methods are developed to transform a large matrix of gene expression levels into a more informative set of which genes are highly possible to share biological properties. Although clustering-based algorithms for microarray data analysis have been extensively studies, most works have not focused on the systematic comparison and validation of clustering results.
Different algorithms tend to lead to different clustering solutions on the same data, while the same algorithm often leads to different results for different parameter settings. Since there is no consensus on choosing among them, the applicable measures should be applied for assessing the quality of a clustering solution in different situations. For example, when the true solution is known and we can compare it to another solution, Minkowski measure [16] or the Jaccard coefficient [17] is applicable. Whereas, when the true solution is not known, there is no agreed-upon method for validating the quality of a suggested solution. Several methods evaluate clustering solutions based on intra-cluster homogeneity or inter-cluster separation [18, 19]. Meanwhile, the prediction of the correct number of clusters is a basic problem in unsupervised classification problems. To solve this problem, a number of cluster validity indices, assessing the quality of a clustering partition have been proposed.
In the present paper, we would like to systematically evaluate various MFs applied to gene-expression data analysis. We compare six MFs, including two orthogonal MFs (i.e. PCA and SVD) and four non-orthogonal MFs (i.e. ICA, NMF and NMF with sparseness constraints (SNMF) and BSNMF) and a well-known unsupervised clustering method, K-means algorithm. All were evaluated by seven cluster-evaluation indices. We evaluated them in view of basic three categories: (1) traditional clustering, (2) orthogonal MFs and (3) non-orthogonal MFs. Predictive power and consistency of the methods are evaluated by using adjusted Rand Index and accuracy index when the class labels of data were available. To evaluate the biological relevance of the resulting clusters from different algorithms, we evaluated the significance of the biological enrichment for the clusters by using Gene Ontology (GO) and biological pathway annotations.
Results
Evaluation of each clustering-based method
Among measures, the GAP statistic is optimized when it decreases (Fig. 1(g)), while others are optimized when they increase (Fig. 1(a) – (f)). The homogeneity, separation, Dunn Index, average silhouette width and Hubert correlation (i.e. Hubert’s gamma) tend to be higher for non-orthogonal MFs than results from orthogonal MFs and K-means algorithm. The GAP statistic is lower for non-orthogonal MFs than orthogonal MFs and K-means. But, Pearson correlation of cophenetic distance has the highest value for SVD (Fig. 1(e)). Overall, non-orthogonal MFs represented best clustering quality.
We compared homogeneity with separation at the same time (Additional File 1). Results from measures for each dataset were clustered. Results from NMF, SNMF and BSNMF showed higher slope, that is, their homogeneity and separation are more optimized than others. When we compare one of the measures, Hubert correlation of cophenetic distance between MFs, at each number of clusters (Additional File 2), NMF, SNMF and BSNMF showed better performance than others in four datasets except for the Leukemia dataset. ICA has the highest value for the Leukemia dataset. Overall, non-negative MFs have best clustering quality.
Class Assignment of Acute Myelogenous Leukemia (AML) and Acute Lymphoblastic Leukemia (ALL)
Kmeans | ^{*}SVD | ^{*}PCA | ^{*}ICA | ^{*}NMF | ^{*}SNMF | ^{*}BSNMF | ^{*}Voting | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
(K=2) | (K=3) | (K=2) | (K=3) | (K=2) | (K=3) | (K=2) | (K=3) | (K=2) | (K=3) | (K=2) | (K=3) | (K=2) | (K=3) | (K=2) | (K=3) | |
ALL_19769_B.cell ALL_23953_B.cell ALL_28373_B.cell ALL_9335_B.cell ALL_9692_B.cell ALL_14749_B.cell ALL_17281_B.cell ALL_19183_B.cell ALL_20414_B.cell ALL_21302_B.cell ALL_549_B.cell ALL_17929_B.cell ALL_20185_B.cell ALL_11103_B.cell ALL_18239_B.cell ALL_5982_B.cell ALL_7092_B.cell ALL_R11_B.cell ALL_R23_B.cell ALL_16415_T.cell ALL_19881_T.cell ALL_9186_T.cell ALL_9723_T.cell ALL_17269_T.cell ALL_14402_T.cell ALL_17638_T.cell ALL_22474_T.cell AML_12 AML_13 AML_14 AML_16 AML_20 AML_1 AML_2 AML_3 AML_5 AML_6 AML_7 | ^{**}L L L L L L L L L L L L L L L L L L L L L L L L L L L L L ^{**}M M L L L M L L M | ^{**}B B B B B B B B B B B B B B B B B B B ^{**}T T T T T T T T B B M M B B B M B B M | M L M M M M L L M L M M L M L L L L M L L L L L L L L L L L L M M L L M L L | B T M B B B M T M T B M M B M T M M B T T T T M T T M M M M T B B M T B M T | L L L L L L L L L L L L L L L L L L L L M M M L M L M L L L L L L L L L L L | M B M B M M M M B B M M M B M B M M B B B T T T B B B M B M M M M M M M M M | L L L L L M L L L L L L L L L L M L L L L L L L L L L M L M M M M M M M M M | B B B B B B B B B B B B B B B B B B B B B T T T B B T M B M M M M M M M M M | L L L L L M L L L L L L L L L L M L L L L L L L L L L M M M M M M M M M M M | B B B B B M B B B T B B B B B B M B B T T T T T T T T M M M M M M M M M M M | L L L L L L L L L L L L L L L L L L L L L L L L L L L M L M M M M M M M M M | B B B B B B B B B T B B B B B B B B B T T T T T T T T M B M M M M M M M M M | L L L L L L L L L L L L L L L L L L L L L L L L L L L M L M M M M M M M M M | B B B B B B B B B B B B B B B B B B B T T T T T T T T M B M M M M M M M M M | L L L L L L L L L L L L L L L L L L L L L L L L L L L M L M M M M M M M M M | B B B B B B B B B B B B B B B B B B B T T T T T T T T M B M M M M M M M M M |
Error Count | 7 | 7 | 18 | 20 | 16 | 18 | 3 | 5 | 2 | 3 | 1 | 2 | 1 | 1 | 1 | 1 |
Class assignment for Medulloblastoma dataset
☐ Sample | Subgroup | Kmeans | ^{*}SVD | ^{*}PCA | ^{*}ICA | ^{*}NMF | ^{*}SNMF | ^{*}BSNMF | ^{*}Voting |
---|---|---|---|---|---|---|---|---|---|
Brain_MD_7 Brain_MD_59 Brain_MD_20 Brain_MD_21 Brain_MD_50 Brain_MD_49 Brain_MD_45 Brain_MD_43 Brain_MD_8 Brain_MD_42 Brain_MD_1 Brain_MD_4 Brain_MD_55 Brain_MD_41 Brain_MD_37 Brain_MD_3 Brain_MD_34 Brain_MD_29 Brain_MD_13 Brain_MD_24 Brain_MD_65 Brain_MD_5 Brain_MD_66 Brain_MD_67 Brain_MD_58 Brain_MD_53 Brain_MD_56 Brain_MD_16 Brain_MD_40 Brain_MD_35 Brain_MD_30 Brain_MD_23 Brain_MD_28 Brain_MD_60 | classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic classic desmoplastic desmoplastic desmoplastic desmoplastic desmoplastic desmoplastic desmoplastic desmoplastic desmoplastic | ^{ ** } 2 ^{ ** }1 1 1 1 2 1 1 1 2 2 2 2 1 1 2 2 1 2 2 1 1 1 1 2 2 2 2 1 2 2 2 1 1 | 2 1 1 2 1 2 2 2 1 1 1 1 1 1 2 2 2 2 1 2 1 1 2 1 2 1 2 1 1 2 2 2 1 2 | 2 1 1 2 2 2 2 2 2 2 2 2 2 1 1 2 2 1 2 2 1 1 1 1 2 2 2 2 2 2 2 2 2 2 | 2 1 1 1 2 2 1 1 1 2 2 2 2 1 1 2 2 1 2 2 1 1 1 1 2 2 2 2 1 2 2 2 2 1 | 2 1 1 1 1 2 1 1 1 2 2 2 2 1 1 2 2 1 2 2 1 1 1 1 2 2 2 2 1 2 2 2 2 1 | 2 1 1 1 1 2 1 1 1 2 2 2 2 1 1 2 2 1 2 2 1 1 1 1 2 2 2 2 2 2 2 2 1 1 | 2 1 1 1 1 2 1 1 1 2 2 2 2 1 1 2 2 1 2 2 1 1 1 1 2 2 2 2 2 2 2 2 2 2 | 2 1 1 1 1 2 1 1 1 2 2 2 2 1 1 2 2 1 2 2 1 1 1 1 2 2 2 2 1 2 2 2 2 2 |
Error Count | 14 | 16 | 16 | 14 | 13 | 13 | 11 | 12 |
Evaluation of biological relevance
To evaluate the biological relevance of the clustering results, we created clusters of genes and assigned them to the corresponding sample-wise clusters. For MFs, we clustered genes by using coefficient matrix of genes. For instance, in the Leukemia dataset factorized by NMF at K=2, we clustered genes into two groups by using the coefficient matrix of genes, W, from NMF. Given such a factorization, the matrix W is able to be used to determine the gene cluster membership, that is, a gene i is placed in a cluster j if the w_{ ij } is the largest entry in row i. Applying K-means algorithm, we clustered genes using original gene expression data matrix. Then, we labelled gene-cluster corresponding to the labels of sample-cluster.
Number of significantly enriched GO terms (or pathways)
(a) Leukemia dataset | |||||||
---|---|---|---|---|---|---|---|
☐ | Kmeans | SVD | PCA | ICA | NMF | SNMF | BSNMF |
ALL | 480 | 389 | 441 | 453 | 532 | 425 | 535 |
AML | 85 | 262 | 223 | 222 | 167 | 266 | 280 |
Total | 565 | 651 | 664 | 675 | 699 | 691 | 815 |
(b) Medulloblastoma dataset | |||||||
☐ | Kmeans | SVD | PCA | ICA | NMF | SNMF | BSNMF |
classic | 517 | 373 | 467 | 479 | 388 | 456 | 599 |
desmoplastic | 58 | 361 | 226 | 213 | 335 | 208 | 206 |
Total | 575 | 734 | 693 | 692 | 723 | 664 | 805 |
(c) Fibroblast dataset | |||||||
☐ | kmeans | SVD | PCA | ICA | NMF | SNMF | BSNMF |
cluster1 | 52 | 45 | 71 | 47 | 57 | 41 | 128 |
cluster2 | 32 | 35 | 68 | 27 | 54 | 48 | 69 |
cluster3 | 48 | 24 | 63 | 61 | 37 | 75 | 50 |
cluster4 | 126 | 38 | 37 | 96 | 108 | 60 | 155 |
cluster5 | 54 | 63 | 60 | 33 | 65 | 68 | 102 |
Total | 312 | 205 | 299 | 264 | 321 | 292 | 504 |
(d) Mouse dataset | |||||||
☐ | kmeans | SVD | PCA | ICA | NMF | SNMF | BSNMF |
cluster1 | 593 | 520 | 294 | 258 | 637 | 686 | 690 |
cluster2 | 27 | 61 | 107 | 114 | 38 | 28 | 56 |
Total | 620 | 581 | 401 | 372 | 675 | 714 | 746 |
The top- ranked genes with the largest coefficient in W matrix of BSNMF may be most explanatory for each cluster (Additional File 3). The top ranked 20 genes for the ALL cluster are enriched in significant GO terms like response to external stimulus, immune response and cell growth. Genes for the AML cluster had are enriched in response to external stimulus, immune response and membrane genes. The gene functions in PubMed indicated that the two sets of 20 genes are enriched in chemokines and tumor suppressor genes. Genes for the first cluster of meduloblastoma were related to cytoplasm, cell motility and cell growth and/or maintenance and those for the second cluster to cytoplasm, biosynthesis and protein metabolism genes. Gene sets for other datasets can be found in the supplement web site.
The mean expression profiles of the gene-wise clusters from the fibroblast dataset were extracted (Additional File 4). We clustered genes by using coefficient matrix of genes when we applied MFs. Coefficient matrix of genes (W matrix) can be used to determine cluster membership of genes, that is, gene i belongs to cluster j if the w_{ ij } is the largest entry in row i. Applying K-means algorithm, we clustered genes using original gene expression data matrix. Then, we labelled gene-cluster corresponding to the labels of sample-cluster. According to method mentioned above, gene-wise clusters were created by the seven methods. Number of gene-wise clusters is five because Xu et al. [21] and Sharan et al. [18] suggested that optimal number of clusters is five from the fibroblast dataset. While K-means, SVD and PCA tend to result a few clusters with dominant profiles with the remaining clusters with relatively flat profiles, non-orthogonal MFs tend to create clusters with even dominance. For example, SVD result shows one major peak and BSNMF result shows much more peaks. Non-orthogonal MFs seem to be more effective in discovering significant patterns.
Discussion
There are various clustering-based methods which are proposed by many researchers. These methods have become a major tool for gene expression data analysis. Different clustering-based methods usually produce different solutions and one or a few preferred solutions among them should be selected. However, a systematic evaluation study for the methods has not been reported. Therefore, we evaluated orthogonal (i.e. PCA, SVD), non-orthogonal (i.e. ICA, NMF and SNMF) MFs and a traditional clustering algorithm (i.e. K-means) using seven clustering-quality (i.e. homogeneity, separation, Dunn index, average silhouette width, Pearson correlation of cophenetic distance, Hubert correlation of cophenetic distance and the GAP statistic) and two prediction-accuracy measures (i.e. the adjusted Rand index and prediction accuracy) applying to five published datasets. We also included an improving non-orthogonal MFs, BSNMF in the evaluation study.
As a result, we observed that clustering quality and prediction-accuracy indices applying non-orthogonal MFs are better than those of orthogonal MFs and K-means. In respect to results from Homogeneity, separation, Dunn index, average silhouette width and Hubert correlation of cophenetic distance, non-orthogonal MFs had higher value than those of orthogonal MFs and K-means. The GAP statistic was lower for non-orthogonal MFs than for orthogonal MFs and K-means. When we tested predictive accuracy for the three datasets with known class labels, we also observed better performance for non-orthogonal MFs than for the rest. We also investigated the biological significance of clustering genes because it is important to discover biological relevant patterns and interpret biologically for analysis of DNA microarray gene expression data. When we used enrichment analysis with GO terms and biological pathways, we obtained more significant enriched GO terms or pathways for non-orthogonal MFs than for orthogonal MFs and K-means. We also identified genes that may be dominantly involved in each subtype. It was demonstrated that BSNMF showed improved performance in prediction-accuracy and biological-enrichment measures, outperforming other non-orthogonal MFs as well as orthogonal MFs and K-means algorithm.
There are various clustering evaluation indices we mentioned. Because they have various results upon datasets, they have limitations to suggest which clustering-based method is the best. Therefore, improving cluster validation indices is needed to overcome it. We simply suggested a voting scheme that simply combines all the results from the various algorithms and returns the best consensus. Improving evaluation indices can be achieved through the integration of results from various evaluation indices using unifying rules.
Conclusions
In conclusion, the clustering performance of orthogonal and non-orthogonal MFs was appropriately compared for clustering microarray data using various measurements. We clearly showed that non-orthogonal MFs have better performance than orthogonal MFs and K-means for clustering microarray data. The characteristic difference among non-orthogonal MFs, orthogonal MFs and K-means algorithm implies that non-orthogonal MFs divided whole data into distinct patterns more evenly than orthogonal MFs and K-means. This study would help for suitably evaluating diverse clustering methods in other genome-wide data as well as microarray data.
Methods
Dataset
For the evaluation study, we used five published datasets. The Leukemia data set [22] has 38 bone marrow samples and 5000 genes after filtering process applied by Brunet et al.[9]. Acute myelogenous Leukemia (AML) and acute lymphoblastic leukemia (ALL) are distinguished as well as ALL can be divided into T and B cell subtypes. The second is Medulloblastoma dataset that is a gene expression profiles from the childhood brain tumors. Although the pathogenesis of the tumor is not well understood, it can be categorized into two known histological subclasses: classic and desmoplastic. Pomeroy et al.[23] demonstrated the correlation of gene expression profiles and the two histological classes. The dataset has 34 samples and over 5800 genes. The third is the gene expression dataset from Zhang et al. (2004, http://hugheslab.med.utoronto.ca/Zhang). This dataset contains gene expression profiles of over 40000 known as well as predicted genes in 55 mouse tissues, organs and cell types. We used over 8200 genes after filtering with low variance. The forth is the human fibroblast gene-expression dataset from Iyer et al.[24] with 18 samples and 517 genes. The last is the well-known Iris dataset [25]. This famous dataset gives the measurements in centimetres of the length and width of sepal and petal, respectively, for 50 flowers from each of the three species of Iris (i.e. Iris setosa, versicolor and virginica). Among datasets, Leukemia, Medulloblastoma and Iris dataset have known class labels for samples, while the rest have not.
Non-orthogonal matrix factorization for gene expression analysis
The gene-expression data is typically represented as an N-by-M matrix A. In the matrix, each row represents the expression values of a gene across all samples. Each column represents the expression values of all genes in a sample. NMF can decompose gene expression data and derive parts-based representation of the whole data. It factorizes a matrix A into the product of two matrices, including non-negative entries, formulated as A = WH. W and H are N-by-K and K-by-M matrices, respectively, and K is much smaller than M. The column of W can be regarded as a metagene, consisting of elements w_{ i }. Each element represents the coefficient of gene i in metagene j. The columns of matrix H represent the metagene expression pattern of the corresponding sample. Each element h_{ ij } indicates the expression value of metagene i in sample j. The cluster membership can be determined based on such a factorization of the matrix H. Sample j belongs to cluster i if the h_{ ij } is the largest entry in column j.
Brunet et al. [9] represented parts corresponding to metagenes which represent genes tend to be co-expressed in samples. Here parts mean sets of elements, indicating the building blocks for the whole. These metagenes can overlap, indicating that a single gene may be involved in a number of pathways or biological processes. Therefore, sparseness constraints are needed. NMF with sparseness constraints has been proposed by a few groups. Gao and Church [14] proposed a method to enforce sparseness of H matrix by penalizing the number of non-zero entries. This method enforces sparseness by combining the goal of minimizing reconstruction error with that of sparseness [14]. Specifically, they adopt the point-count regularization approach that enforces sparseness of H by penalizing the number of non-zero entries rather than the sum of entries ∑h_{ ij } in H [11, 12, 15]. The sparseness is controlled by the parameter and larger parameter makes the H matrix become more and more sparse. Here, the optimization leads the resulting H matrix to contain as many zero entries as possible. Gao’s method enforces sparseness to H matrix only. We applied the sparseness constraints bi-directionally to both W and H. Because microarray gene expression data analysis involves clustering by genes as well as by samples. In microarray data analysis, sample-based clustering can be used to classify samples with similar appearance while gene-based clustering can provide informative sets of tightly co-regulated genes and information about activity of genes. While sample-based clustering relies on metagenes, gene-based clustering relies on meta-samples. The two processes can be viewed as bi-directionally constrained with each other. Good metagene may support good sample-based clusters and vice versa. Optimizing sample-dimension only, sparseness of gene-dimension is relatively decreased when sparseness of sample-dimension is increased. In result, the minimization problem is convex that was subsequently described by others [11, 12, 14, 15] and the resulting matrix cannot support gene-based clusters well. Therefore, optimizing both sample and gene dimension together may be appropriated for clustering of microarray data. This method can optimize both sample and gene clustering. In this paper, we especially focus on BSNMF (Bi-directional Sparseness Non-negative matrix factorization). The definition and algorithm is described below.
Definition: Bi-directional Sparseness Non-negative matrix factorization (BSNMF)
Given a non-negative gene expression data V of size N- by-M, find the non-negative matrices W and H of size N- by-C and C- by-M (respectively) such that
E(W, H) = ||V-WH||^{2}
is minimized, under optional constraints:
Sparseness (w_{ i }) = λ_{1}
Sparseness (h_{ i }) = λ_{2},
where w_{ i } is the i^{th} column of W and h_{ i } is the i^{th} row of H. Here, C denotes the number of components (metagenes), λ_{1} and λ_{2} are the desired sparseness of W and H, respectively. These three parameters are set by the experimenters.
- 1.
Initialize W and H to random positive matrices of dimension N- by-C and C- by-M, respectively.
- 2.
Rescale the column of W and the row of H to unit norm.
- 3.
Iterate until convergence or reach maximum number of allowed iteration.
- (1)
If sparseness constraints on H apply
- a.
solve W_{(}_{ ia }_{+1)} = W_{ ia }(VH^{T})_{ ia }/(WHH^{T})_{ ia }
- b.
Rescale the column of W to unit norm
- c.
Solve for each j
- d.
if (H_{ ij }<0) then H_{ ij } =0
- (2)
If sparseness constraints on W apply,
- a.
solve H_{(}_{ ia }_{+1)} = H_{ ia }(W^{T}V)_{ ia }/(W^{T}WH)_{ ia }
- b.
Rescale the column of H to unit norm
- c.
Solve for each j
- d.
if (W_{ ij }<0) then W_{ ij } =0
Measures of clustering evaluation
In this study, we attempt to evaluate various MFs using cluster evaluation indices. Here, we briefly introduce cluster evaluation indices we used.
In this equation, C is a cluster. C(M) is the cluster centroid and C(x) is each data item. Corr(C(x), C(M)) is the correlation coefficient between each data item and the centroid. N is the number of data items.
Where dist(C_{ k }, C_{ l }) is the minimum distance between a pair of data items, i and j, with i ∈ C_{ k } and j ∈ C_{ l }.
where diam(C_{ m }) is the maximum intra-cluster distance within cluster C_{ m } and dist(C_{ k },C_{ l }) is the minimum distance between pairs of data items, i and j, with i ∈ C_{ k } and j ∈ C_{ l }. The interval of Dunn Index is [0, +∞] and it should be maximized.
where a(i) is the average dissimilarity between i and all other points of the cluster to which i belongs. b(i) is the average dissimilarity of i between all observations in its neighbour cluster. A large s(i) means that data items are “well clustered”.
where M = N(N-1)/2, P is the proximity matrix of the data set and Q is an N-by-N matrix of which (i, j) element represents the distance between the representative points of the clusters where the objects x_{ i } and x_{ j } belong.
K is the total number of clusters giving within dispersion measures W_{ k }, k = 1,2,…, K. The Gap statistic should be minimized to find the ‘optimal’ number of clusters.
where n_{ lk } denotes the number of data items assigned to both cluster l and cluster k. The Adjusted Rand Index has a value in the interval [0, 1] and is to be maximized.
where I (j_{ i }) is 1 if the cluster assignment is correct for sample j_{ i }, otherwise 0 if the cluster assignment is incorrect.
Biological enrichment analysis
We applied biological enrichment analysis to clustering results in order to assess whether functionally related genes are grouped. The resulting genes from clustering are then subdivided into functional categories for biological interpretation. Such functional categorization was accomplished using GO terms and biological pathways. We used DAVID 2.1 (http://david.abcc.ncifcrf.gov/) for GO term enrichment analysis and ArrayXPath [40, 41] for pathway annotation. A modified Fisher’s exact test is performed to determine whether the proportions of members falling into each category differ by group, when those in two independent groups fell into one of the two mutually exclusive categories. Therefore, lower p-value indicates a better association of cluster members.
Declarations
Acknowledgements
This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (No.2011-0018257), Systems Biomedical Informatics National Core Research Center and a grant of the Korea Healthcare technology R&D Project, Ministry of Health & Welfare, Republic of Korea (A070001).
This article has been published as part of BMC Bioinformatics Volume 12 Supplement 13, 2011: Tenth International Conference on Bioinformatics – First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Bioinformatics. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105/12?issue=S13.
Authors’ Affiliations
References
- Bicciato S, Luchini A, Di Bello C: PCA disjoint models for multiclass cancer analysis using gene expression data. Bioinformatics 2003, 19(5):571–578. 10.1093/bioinformatics/btg051View ArticlePubMedGoogle Scholar
- Qi Q, Zhao Y, Li M, Simon R: Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools. Bioinformatics 2009, 25(4):545–547. 10.1093/bioinformatics/btp009View ArticlePubMedGoogle Scholar
- Schachtner R, Lutter D, Knollmuller P, Tome AM, Theis FJ, Schmitz G, Stetter M, Vilda PG, Lang EW: Knowledge-based gene expression classification via matrix factorization. Bioinformatics 2008, 24(15):1688–1697. 10.1093/bioinformatics/btn245PubMed CentralView ArticlePubMedGoogle Scholar
- Tan Y, Shi L, Tong W, Hwang GT, Wang C: Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. Comput Biol Chem 2004, 28(3):235–244. 10.1016/j.compbiolchem.2004.05.002View ArticlePubMedGoogle Scholar
- Ma S, Dai Y: Principal component analysis based methods in bioinformatics studies. Brief Bioinform 2011.Google Scholar
- Paatero P, Tapper U: Positive matrix factorization: A non-negative factor model with optimal utilization of errorest mates of data values. Environmetrics 1994, 5: 111–126. 10.1002/env.3170050203View ArticleGoogle Scholar
- Lee DD, Seung HS: Learning the parts of objects by non-negative matrix factorization. Nature 1999, 401(6755):788–791. 10.1038/44565View ArticlePubMedGoogle Scholar
- Hyvarinen A, Karhunen J, Oja E: Independent Component Analysis. In Edited by: Interscience W. 2001.View ArticleGoogle Scholar
- Brunet JP, Tamayo P, Golub TR, Mesirov JP: Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci U S A 2004, 101(12):4164–4169. 10.1073/pnas.0308531101PubMed CentralView ArticlePubMedGoogle Scholar
- Li SZ, Hou XW, Zhang HJ, Cheng QS: Learning spatially localized parts-based representation. Proceedings of IEEE International Conference on Computer Vision and Pattern Recognition: December 2001 2001 2001, 207–212.Google Scholar
- Hoyer PO: Non-negative sparse coding. Neural Networks for Signal Processing XII: 2002; Martigny, Switzerland 2002, 557–565.View ArticleGoogle Scholar
- Hoyer PO, Dayan P: Non-negative Matrix Factorization with sparseness constraints. Journal of Machine Learning Research 2004, 5: 1457–1469.Google Scholar
- Wang Y, Jia Y, Hu C, Turk M: Fisher non-negative matrix factorization for learning local features. In Asian Conference on Computer Vision. Jeju, Korea; 2004:806–811.Google Scholar
- Gao Y, Church G: Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics 2005, 21(21):3970–3975. 10.1093/bioinformatics/bti653View ArticlePubMedGoogle Scholar
- Pauca P, Shahnaz F, Berry M, Plemmons R: Text Mining using Non-Negative Matrix Factorizations. Proceedings of the Fourth SIAM International Conference on Data Mining: April 22–24 2004; Lake Buena Vista, Florida, USA 2004.Google Scholar
- Sokal RR: Clustering and classification: background and current directions. In Classification and Clustering. Edited by: Van Ryzin J. Academic Press, London; 1977:1–15.Google Scholar
- Everitt BS: Cluster Analysis. Edward Arnold; 1933.Google Scholar
- Sharan R, Maron-Katz A, Shamir R: CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics 2003, 19(14):1787–1799. 10.1093/bioinformatics/btg232View ArticlePubMedGoogle Scholar
- Yeung KY, Haynor DR, Ruzzo WL: Validating clustering for gene expression data. Bioinformatics 2001, 17(4):309–318. 10.1093/bioinformatics/17.4.309View ArticlePubMedGoogle Scholar
- Dueck D, Morris QD, Frey BJ: Multi-way clustering of microarray data using probabilistic sparse matrix factorization. Bioinformatics 2005, 21(Suppl 1):i144–151. 10.1093/bioinformatics/bti1041View ArticlePubMedGoogle Scholar
- Xu Y, Olman V, Xu D: Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics 2002, 18(4):536–545. 10.1093/bioinformatics/18.4.536View ArticlePubMedGoogle Scholar
- Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al.: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286(5439):531–537. 10.1126/science.286.5439.531View ArticlePubMedGoogle Scholar
- Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, et al.: Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 2002, 415(6870):436–442. 10.1038/415436aView ArticlePubMedGoogle Scholar
- Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JC, Trent JM, Staudt LM, Hudson J Jr., Boguski MS, et al.: The transcriptional program in the response of human fibroblasts to serum. Science 1999, 283(5398):83–87. 10.1126/science.283.5398.83View ArticlePubMedGoogle Scholar
- Fisher R: The use of multiple measurements in taxonomic problem. Ann Eugenics 1936, 7: 179–188. 10.1111/j.1469-1809.1936.tb02137.xView ArticleGoogle Scholar
- Bezdek J, Pal N: Some new indexes of cluster validity. IEEE Trans Syst Man Cybernet 1998, 28: 301–315. 10.1109/3477.678624View ArticleGoogle Scholar
- Halkidi M, Batistakis Y, Vazirgiannis M: On clustering validation techniques. Journal of Intelligent Information Systems 2001, 17: 107–145. 10.1023/A:1012801612483View ArticleGoogle Scholar
- Dunn J: Well separated clusters and optimal fuzzy partitions. Journal of Cybernetics 1974, 95–104.Google Scholar
- Davies DL, Bouldin DW: Acluster separation measure. IEEE Trans Pattern Anal Machine Intell 1979, 1: 224–227.View ArticleGoogle Scholar
- Rousseeuw PJ: Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 1987, 20: 53–65. 10.1016/0377-0427(87)90125-7View ArticleGoogle Scholar
- Romesburg HC: Cluster Analysis for Researchers. Belmont, Calif.: Lifetime Learning Publications; 1984.Google Scholar
- Edwards AL: The Correlation Coefficient. In An Introduction to Linear Regression and Correlation. San Francisco, CA: W. H. Freeman; 1976.Google Scholar
- Lehmann EL, D'Abrera HJM: Nonparametrics: Statistical Methods Based on Ranks. Upper Saddle River, N.J. : Prentice Hall; 1998.Google Scholar
- Tibshirani R, Walther G, Hastie T: Estimating the number of clusters in a data set via the gap statistic. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 2001, 63(2):411–423. 10.1111/1467-9868.00293View ArticleGoogle Scholar
- Rand WM: Objective criteria for the evaluation of clustering methods. Journal of the American Statistical Association 1971, 66(336):846–850. 10.2307/2284239View ArticleGoogle Scholar
- Hubert A: Comparing partitions. J Classif 1985, 2: 193–198. 10.1007/BF01908075View ArticleGoogle Scholar
- Jaccard S: Nouvelles recherches sur la distribution florale. Bull Soc Vandoise des Sci Nat 1908, 44: 223–270.Google Scholar
- Jardine N, Sibson R: Mathematical Taxonomy. Wiley, London. Kangas; 1971.Google Scholar
- Xu W, Liu X, Gong Y: Document-clustering based on non-negative matrix factorization. Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval July 28- August 1 2003; Toronto, CA 2003, 267–273.Google Scholar
- Chung HJ, Kim M, Park CH, Kim J, Kim JH: ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res 2004, 32(Web Server issue):W460–464.PubMed CentralView ArticlePubMedGoogle Scholar
- Chung HJ, Park CH, Han MR, Lee S, Ohn JH, Kim J, Kim JH: ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res 2005, 33(Web Server issue):W621–626.PubMed CentralView ArticlePubMedGoogle Scholar
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