PathAct: a novel method for pathway analysis using gene expression profiles

Abstract

We developed PathAct, a novel method for pathway analysis to investigate the biological and clinical implications of the gene expression profiles. The advantage of PathAct in comparison with the conventional pathway analysis methods is that it can estimate pathway activity levels for individual patient quantitatively in the form of a pathway-by-sample matrix. This matrix can be used for further analysis such as hierarchical clustering and other analysis methods. To evaluate the feasibility of PathAct, comparison with frequently used gene-enrichment analysis methods was conducted using two public microarray datasets. The dataset #1 was that of breast cancer patients, and we investigated pathways associated with triple-negative breast cancer by PathAct, compared with those obtained by gene set enrichment analysis (GSEA). The dataset #2 was another breast cancer dataset with disease-free survival (DFS) of each patient. Contribution by each pathway to prognosis was investigated by our method as well as the Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis. In the dataset #1, four out of the six pathways that satisfied p < 0.05 and FDR < 0.30 by GSEA were also included in those obtained by the PathAct method. For the dataset #2, two pathways (“Cell Cycle” and “DNA replication”) out of four pathways by PathAct were commonly identified by DAVID analysis. Thus, we confirmed a good degree of agreement among PathAct and conventional methods. Moreover, several applications of further statistical analyses such as hierarchical cluster analysis by pathway activity, correlation analysis and survival analysis between pathways were conducted.

Background

Gene expression profiling by microarray analysis provides a huge amount of biological information and has been widely used in biological and clinical research. Since microarray technique simultaneously detects expression levels for more than ten thousand of genes, bioinformatics approaches for interpretation of such large-scale data are essential. The microarray data is often examined using the information of a pathway, which represents a series of biological reactions that causes a specific event such as signal transduction, cell proliferation, and drug metabolism. There are several pathway databases such as the KEGG PATHWAY database [1], BioCarta [2] and GenMAPP [3]. In addition, Gene Ontology (GO) database [4] provides controlled vocabularies of various genes and has a hierarchical structure based on their functions. Recently, several interpretation tools such as gene set enrichment analysis (GSEA) [5], the Database for Annotation, Visualization and Integrated Discovery (DAVID) [6], GenMAPP [3], and GOMiner [7] have been developed and widely used in the microarray analysis. The majority of tools for pathway analysis detect pathway-level difference between two groups (e.g., cases and controls). The output results generated by these tools are typically given as a list of p-values and other softwarespecific information, which is not suitable for further analyses. If the activity (i.e., the degree of up- and down-regulation) of a pathway can be estimated in each samples, these information would be of great use for investigation of patient-specific characteristics of a disease and further development of personalized medicine. In this study, a novel method for pathway analysis, called PathAct, is introduced. PathAct can estimate individual pathway activity by conversion of gene expression data into quantitative values for both of each pathway and each sample. One of the most unique features is that the output data is given in matrix form, which can be used for further analysis such as hierarchical clustering and other multivariate analysis methods.

The median polish (MP) algorithm [8], which is a core component in PathAct, is a suitable method for an additive decomposition of a two-dimensional data matrix. MP is known as an exploratory data analysis for extraction of both row-wide and column-wide trends from a two-dimensional matrix. MP is an iterative procedure that consists of the following four steps: (1) calculating median values of each row, (2) subtracting the median values from each row, (3) calculating median values of each column, and (4) subtracting the median values from each column. These steps are repeated using the residual matrix as a new data, and the median vectors for the row and the column are accumulated at each iteration. This procedure is iterated until the reduction of the sum of absolute residual is less than a specified value, or the maximum limit of iteration is exceeded. The MP method has been used for several bioinformatics tools including the robust multi-array average (RMA) method [9], one of the most well-known normalization methods for DNA microarray data.

Methodology

PathAct algorithm:

Application of the MP method to microarray data is formularized as follows. Suppose that a pathway p contains N_p genes, and M samples are obtained from the microarray experiment. Note that a gene may belong to multiple pathways. For the N_p×M gene expression matrix G_p, the expression intensity of the i-th gene for the j-th individual is denoted as G_{p[i, j]}. Using MP, G_p is decomposed into a gene effect g_p[i], an individual effect a_p[j], and an residual matrix R_{p[i, j]}, G_{p[i, j]} = g_p[i] + a_p[j] + R_{p[i, j]}; The individual effect ap is the pathway activity and is used for further analysis. The gene effect gp reflects a degree of bias such as hybridization efficiency of each gene. When a database contains K pathways, these steps are repeated for K times to produce the K×M pathway activity matrix A by collecting a_p of each pathway. These procedures, namely PathAct, were implemented in R statistical language version 2.15.2 (http://www.r-project.org/). The program is freely available upon request. A dataset including 229 human pathways was obtained from the KEGG PATHWAY database using an R packages “KEGG.db” and “hgu133plus2.db”. “KEGG.db” contains information about KEGG PATHWAY entry such as pathway IDs and names, whereas “hgu133plus2.db” is an annotation data for Affymetrix HG-133 plus 2.0 array including pathway information. When multiple probe sets correspond to a single gene, a probe set with the largest interquartile range (IQR) was selected as a responsible probe set for the gene. Termination conditions of each MP process were set to 1% as a change of absolute residual and ten times as the maximum iteration steps.

Application to clinical microarray datasets:

To evaluate the feasibility of our pathway analysis method, two public microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database (http:// www.ncbi.nlm.nih.gov/geo/). The dataset #1 (GSE19615) contains a total of 115 gene expression profiles obtained from tissue specimens of breast cancer patients [10] using HG-133 Plus 2.0 arrays. The data have clinicopathological information for estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expressions. Triple-negative breast cancer (TNBC), which does not express ER, PR, and HER2, is associated with higher risk of distant metastasis and poor prognosis compared to other type of breast cancer (non-triplenegative breast cancer; NTNBC) [11]. Therefore, we aimed to identify pathways differently activated between TNBC and NTNBC. The gene expression profiles including 54,613 probe sets were converted into a pathway activity matrix using PathAct. Association between pathway activities and TNBC was determined by the Wilcoxon exact rank-sum test provided by “exactRankTests” package in R. Then, pathways with at least 1.1-fold increase or decrease between TNBC and NTNBC were further selected. The dataset #2 (GSE21653) contains a total of 266 gene expression profiles from breast cancer patients using HG-133 Plus 2.0 arrays [12]. Among them, 252 patients had information for disease-free survival (DFS), which was calculated from the date of diagnosis until date of first relapse or date of death (when the relapse was not observed). These gene expression profiles were also converted into a pathway activity matrix using PathAct, and we investigated pathways associated with DFS using Cox proportional hazards model. In both datasets, pathways satisfying both p < 0.05 by Wald test and FDR < 0.30 were considered statistically significant.

Comparison with conventional pathway analysis methods:

For the dataset #1, we investigated pathways associated with TNBC by gene set enrichment analysis (GSEA) [5]. We used a collection of gene sets for KEGG pathways provided by MSigDB 3.1 (c2.cp.kegg.v3.1.symbols.gmt, available at http://www.broadinstitute.org/gsea/msigdb/). Pathways that satisfied both p < 0.05 and FDR < 0.30 were selected and were compared with the results obtained by PathAct. In the second analysis using dataset #2, as GSEA cannot conduct survival analysis, we first extracted genes related to DFS by Cox proportional hazards model using a cut-off value of p < 0.05 by Wald test. Then, the selected genes were analyzed by DAVID Functional Annotation Tool [6] version 6.7. We used the “KEGG_PATHWAY” category provided by DAVID for analysis of pathways that were overrepresented by the genes associated with DFS. Two separate analyses were performed for the genes up-regulated in poor prognosis patients (hazards ratio (HR) > 1 by the Cox regression) and for those down-regulated in poor prognosis patients (HR < 1). Pathways that satisfied both p < 0.05 and FDR < 0.30 by DAVID analysis were then selected.

Discussion

Pathway-based analysis of TNBC dataset:

Using the dataset #1, we calculated the pathway activity matrix of 229 KEGG pathways for the 115 patients by the PathAct method. We then identified 15 up-regulated and 13 downregulated pathways in TNBC by comparing the pathway activity values between TNBC and NTNBC. Using the calculated pathway activity levels, we next performed a hierarchical cluster analysis using the above 28 pathways (Figure 1A). When the patients were classified into two major clusters, the left cluster contained four TNBC and 61 NTNBC patients, whereas the right cluster contained 26 TNBC and 24 NTNBC patients (p < 0.001 by Fisher's exact test). This indicates that the PathAct method can summarize the important molecular information in breast cancer, a part of which is necessary for classification of TNBC from NTNBC.

Figure 1.

Hierarchical clustering of pathways using output data generated by PathAct. The pathway activity data was transformed into z-scores by setting the mean expression intensities to 0 and variances to 1 for all pathways. The Euclidean distance was used to calculate a similarity matrix among pathways or individuals, respectively. The red dashed lines indicate the two major clusters obtained by the hierarchical cluster analysis. A: a hierarchical cluster analysis using the selected 28 pathways for the dataset #1. B: a hierarchical cluster analysis using the selected 14 pathways for the dataset #2.

Pathways associated with TNBC:

The pathways associated with cell proliferation (e.g., “DNA replication” and “Cell cycle”) and transcription process (e.g., “Basal transcription factors” and “RNA polymerase”) were significantly up-regulated in TNBC Table 1 (see supplementary material). This suggests that the cancer cells in TNBC are more aggressive than those in other type of cancer. On the other hand, the pathway “ECM-receptor interaction”, related to cell adhesion, was down-regulated in TNBC Table 1. Because loss of cell adhesion promotes migration, invasion and metastasis of cancer cells, the down-regulation of these pathways suggested the higher metastatic ability of TNBC than NTNBC. It has been reported that TNBC are further classified into several subtypes such as basal-like, normal-like, and claudin-low subtypes [13]. Among them, the claudin-low subtype shows lower mRNA expression levels of cell cyclerelated genes [14]. As shown in Figure 1A, a part of TNBC patient's exhibits lower activity levels of cell cycle-related Pathways, which suggest the existence of subtypes among TNBC patients.

Pathway-based analysis of DFS in breast cancer:

Using the dataset #2, we also obtained the pathway activity matrix of 229 KEGG pathways for the 266 patients by the PathAct method. Using the pathway activity levels, we selected 14 pathways that had significant association with DFS Table 2 (see Supplementary material). Among these pathways, nine showed hazard ratio (HR) > 1, and the other five had HR < 1. Similar to the analysis of the dataset #1, we conducted a hierarchical cluster analysis using the selected 14 pathways (Figure 1B). When the patients were divided into the two clusters, the left cluster contained 27 recurrence and 80 recurrence-free patients, whereas the right cluster contained 56 recurrence and 89 recurrence-free patients (p = 0.030 by Fisher's exact test). This indicated that the patients in the right cluster had significantly higher risk of tumor recurrence.

Pathways associated with prognosis of breast cancer:

The pathways associated with cell proliferation (e.g., “DNA replication”, “Base excision repair”, and “Cell cycle”) were positively correlated with poor prognosis Table 2. Promotion of cell proliferation in cancer is a typical phenomenon in carcinogenesis and cancer progression. On the other hand, the five pathways for better prognosis contained “Asthma” and “Graft-versus-host disease”, which did not seem to be associated with cancer. However, these pathways include genes related to immune response process such as antigen processing (e.g., MHC class II genes) and cytokines (e.g., IL2, 4, 5, and 9). This suggested that the immune response function in cancerous tissue was activated in patients with better prognosis compared with patients with poor prognosis. In fact, it has been reported that breast cancer patients with a higher number of tumorinfiltrating CD8(+) lymphocytes shows better prognosis [15]. Therefore, activation of these pathways in patients with good prognosis is possibly caused by increased number of lymphocytes by lymphocytic infiltration.

Comparison to conventional methods:

In order to validate the PathAct method, we compared the analysis results of the datasets #1 and #2 with other approaches. First, we performed GSEA for the dataset #1 and identified six pathways that were significantly altered in TNBC Table 3 (see supplementary material). Interestingly, four out of six pathways identified by GSEA were also included in those obtained by the PathAct method. Therefore, we confirmed that GSEA and PathAct had ability to detect common biological pathways in the microarray dataset. Next, we evaluated pathways associated with DFS in the dataset #2. Using Cox proportional hazards model, 1,487 probe sets were identified to be negatively correlated with DFS, whereas 1,081 probe sets had positive correlation with DFS. DAVID analysis was then performed for each of the selected gene sets Table 4 (see supplementary material. “Cell Cycle” and “DNA replication” pathways were significantly overrepresented in genes associated with poor prognosis, and these were also detected by the PathAct method. Similarly, 13 pathways were identified for genes correlated with good prognosis, and four pathways associated with immune response (“Asthma”, “Graft-versushost disease”, “Allograft rejection”, and “Type I diabetes mellitus”) were also detected by the PathAct. Thus, we confirmed good agreement between PathAct and DAVID.

Quantitative analyses using pathway activities:

A major advantage of PathAct method is that obtained pathway activity levels can be used for further statistical analysis. For example, the correlation analysis of “DNA replication” and “Cell cycle” for the dataset #1 was performed (Figure 2A). These two pathways showed significant correlation (p < 0.001 by Pearson's correlation test), and both pathways were up-regulated in TNBC compared with NTNBC. Another example is an analysis of correlation between DFS and the pathway activity in “Allograft rejection” (Figure 2B). When the median value of the pathway activity levels was chosen for a cut-off point, it was demonstrated that up-regulation of this pathway contribute to better prognosis (p = 0.034 by log-rank test). Because the “Allograft rejection” pathway contains many genes associated with immune response, this result infers that increased number of lymphocytes by lymphocytic infiltration could contribute to the better prognosis of the breast cancer patients.

Figure 2.

Application of PathAct method for further numerical analysis. A: correlation analysis of “DNA replication” and “Cell cycle” for the dataset #1 (p < 0.001 by Pearson's correlation test). B: analysis of correlation between DFS and the pathway activity in “Allograft rejection”. Down-regulation of this pathway contribute to better prognosis (p = 0.034 by log-rank test).

Conclusion

Pathway analysis plays an important role in interpreting genome-wide gene expression data. Several methods for pathway analysis have been proposed, but they are restricted to making comparisons between groups. Thus, the development of a flexible evaluation framework for individual patients is crucial for the advanced interpretation of microarray data. In this study, a novel approach for estimating individual pathway activity using the median polish algorithm was introduced. Using the clinical microarray datasets, the capability of the PathAct method was evaluated. The PathAct method could detect the similar pathways with those obtained by the conventional methods such as GSEA and DAVID. Moreover, because the processed data (i.e., the pathway activity matrix) are given as quantitative values for both of each pathway and each sample, they could be utilized for further statistical analysis including analysis of correlation and survival data. Therefore, PathAct is a promising tool for pathway-level investigation and interpretation of the comprehensive gene expression data.

Conflict of interest

No conflict of interest was declared.