A filter-based feature selection approach for identifying potential biomarkers for lung cancer
© Lee et al; licensee BioMed Central Ltd. 2011
Received: 8 October 2010
Accepted: 21 March 2011
Published: 21 March 2011
Lung cancer is the leading cause of death from cancer in the world and its treatment is dependant on the type and stage of cancer detected in the patient. Molecular biomarkers that can characterize the cancer phenotype are thus a key tool in planning a therapeutic response. A common protocol for identifying such biomarkers is to employ genomic microarray analysis to find genes that show differential expression according to disease state or type. Data-mining techniques such as feature selection are often used to isolate, from among a large manifold of genes with differential expression, those specific genes whose differential expression patterns are of optimal value in phenotypic differentiation. One such technique, Biomarker Identifier (BMI), has been developed to identify features with the ability to distinguish between two data groups of interest, which is thus highly applicable for such studies.
Microarray data with validated genes was used to evaluate the utility of BMI in identifying markers for lung cancer. This data set contains a set of 129 gene expression profiles from large-airway epithelial cells (60 samples from smokers with lung cancer and 69 from smokers without lung cancer) and 7 genes from this data have been confirmed to be differentially expressed by quantitative PCR. Using this data set, BMI was compared with various well-known feature selection methods and was found to be more successful than other methods in finding useful genes to classify cancerous samples. Also it is evident that genes selected by BMI (given the same number of genes and classification algorithms) showed better discriminative power than those from the original study. After pathway analysis on the selected genes by BMI, we have been able to correlate the selected genes with well-known cancer-related pathways.
Our results show that BMI can be used to analyze microarray data and to find useful genes for classifying samples. Pathway analysis suggests that BMI is successful in identifying biomarker-quality cancer-related genes from the data.
Lung cancer accounts for large portion of cancer deaths (29%) in the United States for men as well as woman . The major types of lung cancer are small-cell and non-small-cell cancer. Non-small-cell cancer can be further divided into three histological subtypes: squamous-cell carcinoma, adenocarcinoma and large cell lung cancer . Regardless of subtype, the 5-year survival rate for lung cancer is among the lowest of all cancers at 15% (data for USA) . Since the treatment of lung cancer depends on the subtype and the stage of cancer, it is important to have determined specific molecular biomarkers that can identify the type of cancer as a function of genes closely related to each distinct phenotype.
With advance of microarray technologies, it is possible to conduct high throughput determination of the relative rates with which genes are expressed in a given cell or tissue type. This can help researchers better understand a disease at the genomic level and has become an important tool in biological sciences as well as medical and pharmaceutical research. In the context of lung cancer, microarray technology can be used to identify genes whose expression profile in a type of cancer differs from normal tissues or from other types of cancer. Such biomarkers are important since they can provide the basis for improving a diagnostic classifier or for enhancing the prediction of patient-specific prognosis or therapeutic response . From an informatics perspective, the process of selecting differentially expressed genes is readily achieved via data-mining techniques known as feature selection. Feature selection, an important step in the data-mining process, aims to find representative feature subsets that meet desired criteria. In microarray data analysis, one criterion for a desired feature subset would be a set of genes whose expression patterns vary significantly when compared across different sample groups. The resulting subset can then be used to further analysis such as building a diagnostic classifier.
Feature selection methods, in general, can be categorized into three types, depending on how they are combined with other analysis steps: filter methods, wrapper methods and embedded methods . Filter methods assess the relevance of features as scores by looking only at the properties of the data. Features can be sorted by their scores and low-scoring features can be removed. Wrapper methods embed the analysis model within the feature subset search. In this setup, a subset of features is evaluated by applying a specific analysis model to reduced data with the selected feature subset. In embedded methods, the search for an optimal feature subset is built into the analysis algorithm. Filter methods are the most commonly applied in bioinformatics studies since they are computationally simple, fast and independent of other analysis algorithms. Also they allow features to be quantified and prioritized according to the scores, which is particularly important for biological interpretation.
In this paper, a filter-based feature selection method, biomarker identifier (BMI), is adopted to analyze gene expression data that might be used to discriminate between samples with and without lung cancer. The data consists of gene expression patterns in histologically normal large-airway epithelial cells obtained via bronchoscopy from smokers. Genes identified using this data set can be used to diagnosing lung cancer among smokers with suspected lung cancer. The genes selected by BMI were compared with those from various other feature selection algorithms and those identified from the original experimental study. Pathway analysis for the genes selected by BMI was also performed.
Here, λ is a scaling factor and TP2 is the product of the true positive (TP) rates determined for each groups using logistic regression of the form 'outcome ~ feature'. CV ctr and CV denote the coefficient of variance for the feature x in the 'control' group and in both groups, respectively. Also, Δ = , where , and denote the mean value of x in 'control' and in both groups, respectively. For biological data such as microarray, the sign of Δ diff for a particular gene can be interpreted as over-expression or under-expression in 'experiment' compared to 'control'; positive as over-expression and negative as under-expression.
BMI has shown promising results on various data sets such as mass spectrometry data of metabolites , liver disease  and microarray data from various types of cancer . In this study, it is used to identify potential biomarkers for lung cancer from microarray data.
Other feature selection methods
For comparison with BMI, we used 6 different popular feature selection methods: information gain (IG), Relief-F (RF), t-test (T) and its two variants (moderated t-test (MT) and window t-test (WT)), and chi-squared test (CS).
Specifically, it measures the difference between the marginal distribution of observable y assuming that it is independent of feature x (P(y)) and the conditional distribution of y assuming that it is dependent of x (P(y|x)). If x is not differentially expressed, y will be independent of x, thus x will have small information gain value, and vice versa.
Relief-F  is an instance-based feature selection method which evaluates a feature by how well its value distinguishes samples that are from different groups but are similar to each other. For each feature x, Relief-F selects a random sample and k of its nearest neighbors from the same class and each of different classes. Then x is scored as the sum of weighted differences in different classes and the same class. If x is differentially expressed, it will show greater differences for samples from different classes, thus it will receive higher score (or vice versa).
t-test and variants
The Student's t-test  is traditionally used to compare two normally distributed samples or populations. It prefers features with a maximal difference of mean value between groups and a minimal variability within each group, but it can fail when there are small number of samples or the estimated variances are not equal between groups (heteroscedasticity): scenarios which are common for practical data. To cope with such problems, Welch proposed a variant of t-test taking heteroscedasticity into account . Various statistical tests for differential expression are based on the traditional Student and Welch tests. Smyth  applied a hierarchical Bayesian approach (moderated t-test) to the Student and Welch tests and integrated more a priori information to yield more robust estimates. Berger et al.  suggested a window t-test that uses multiple genes which share a similar expression level to compute the variance to be incorporated in the t-test. In this work, we chose Welch's t-test, moderated t-test and window t-test for comparison.
Chi-squared test is another popular statistical test of the divergence between the observed and expected distribution of a feature. In feature selection, it tests whether the distribution of a feature differs between groups. The chi-square score uses the summation of squared differences between observed and expected values divided by expected values.
Spira et al. reported gene expression data from large airway epithelial cells by microarray analysis . This data set covers a set of 129 Affymetrix HG-U133A microarrays comparing 60 smokers with lung cancer and 69 smokers without lung cancer. This experiment was designed to determine if gene expression in histologically normal large-airway epithelial cells obtained via bronchoscopy from smokers with suspected lung cancer could be used as a lung cancer biomarker. In this data set, 7 genes were confirmed to be differentially expressed between cancerous samples and non-cancerous samples by quantitative PCR . The Robust Multichip Average (RMA) algorithm  was used for background adjustment, normalization, and probe-level summarization of the microarray samples (please refer to supplementary methods of  for detailed information). The data set can be accessed from gene expression omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) under accession number of GSE4115. This data set was chosen since it consisted of a significant number of replicates and some of the genes in the data set were confirmed by quantitative PCR, which provides a good basis for preliminary validation.
To contrast performance among feature selection methods, we also used the dataset published through MicroArray Quality Control project phase II (MAQC-II). Among 9 non-control data sets from MAQC-II, the data set with the most balanced number of positive/negative samples (breast cancer data with estrogen receptor status as class) was chosen. The data set consists of training (130 samples) and validation (100 samples) sets. The processed data was obtained through GEO under accession number GSE20194.
Results and Discussion
Comparison with other feature selection methods
Feature selection methods can be evaluated in various ways. One popular way is to observe the classification performance using the features selected by the method. If a feature selection method is able to choose truly significant features, the classifier trained using those features should show good performance with a small number of features. If important features are already known, on the other hand, we can evaluate feature selection methods by how they rank those known features. Since important features have not been reported for the MAQC-II data set, it can be approached only via the first evaluation strategy, but the airway data set is amenable to both modes of evaluation since some of genes have been experimentally confirmed to be differentially expressed.
Comparison of classification performances on MAQC-II data set
Feature Selection Methods
Support Vector Machine
Comparison of classification performances on airway data set
Feature Selection Methods
Support Vector Machine
From these results, it can be said that BMI shows competitive performance in identifying useful features for classification and shows high consistency with actual differential expression.
Comparison with biomarkers from literature
Top 10 genes selected by BMI
early growth response 1
karyopherin alpha 1 (importin alpha 5)
mitogen-activated protein kinase kinase 4
ribosomal protein L23a pseudogene 13
interleukin 13 receptor, alpha 1
alcohol dehydrogenase 6 (class V)
Full length insert cDNA clone YI46D09
ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1
Classification performances with selected biomarkers by BMI and original literature
Biomarkers by BMI
Biomarkers from original literature
Pathway analysis of selected biomarkers
Although a set of genes is useful for training classifier, the constituent genes may be useless as biomarkers if their biological roles are not related to the target disease or process. Thus we analyzed the pathways associated with 80 highly-ranked genes to investigate their biological roles. For pathway analysis, we investigated associated terms in KEGG pathways , NCI-Nature pathway interaction database , and PANTHER (protein analysis through evolutionary relationships) classification system  using the EGAN program .
KEGG pathways and PANTHER classifications associated with top 80 genes selected by BMI
KEGG pathway name
FOS, MSH2, APC
Pathways in cancer
FOS, MSH2, APC, TCEB2
ADH6, SAT1, EXT2, TGDS, BTD, PRPS1, AGPS
MAPK signaling pathway
DUSP10, MAP2K4, FOS
Cytokine-cytokine receptor interaction
CXCR4, ACVR2A, IL13RA1
Toll-like receptor signaling pathway
PPP2R2 D, INADL
Glycosaminoglycan biosynthesis - heparan sulfate
Pentose phosphate pathway
Oxidative stress response
TXN, MAP2K4, DUSP10
T cell activation
Interleukin signaling pathway
Apoptosis signaling pathway
FGF signaling pathway
Axon guidance mediated by Slit/Robo
Hypoxia response via HIF activation
Insulin/IGF pathway-mitogen activated protein kinase kinase/MAP kinase cascade
NCI-Nature pathway interactions associated with top 80 genes selected by BMI
NCI-Nature Pathway Interaction
ATF-2 transcription factor network
ATF3, FOS, DUSP10
Downstream signaling in naïve CD8+ T cells
B2 M, EGR1, FOS
Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met)
EGR1, MAP2K4, APC
Ephrin B reverse signaling
ErbB1 downstream signaling
MAP2K4, FOS, EGR1
Regulation of p38-alpha and p38-beta
Direct p53 effectors
APC, MSH2, ATF3
Trk receptor signaling mediated by the MAPK pathway
RhoA signaling pathway
IL6-mediated signaling events
Presenilin action in Notch and Wnt signaling
Calcineurin-regulated NFAT-dependent transcription in lymphocytes
Regulation of Androgen receptor activity
Fc-epsilon receptor I signaling in mast cells
IL12-mediated signaling events
B2 M, FOS
HIF-1-alpha transcription factor network
CDC42 signaling events
Regulation of nuclear SMAD2/3 signaling
Glucocorticoid receptor regulatory network
Sumoylation by RanBP2 regulates transcriptional repression
JNK signaling in the CD4+ TCR pathway
Ras signaling in the CD4+ TCR pathway
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha
Cellular roles of Anthrax toxin
VEGFR3 signaling in lymphatic endothelium
PDGFR-alpha signaling pathway
ALK1 signaling events
Signaling events mediated by PRL
TRAIL signaling pathway
Regulation of CDC42 activity
Canonical Wnt signaling pathway
p38 MAPK signaling pathway
Calcium signaling in the CD4+ TCR pathway
Nongenotropic Androgen signaling
Nephrin/Neph1 signaling in the kidney podocyte
IL12 signaling mediated by STAT4
In this work, a filter-based feature selection method, biomarker identifier (BMI), has been applied to find potential biomarkers for lung cancer from microarray data. BMI measures the potential value of each gene as a biomarker candidate by combining various statistical measures to assess its ability to distinguish between two data groups of interest. We evaluated BMI performance on two public microarray data sets: one from the MicroArray Quality Control project and the other from smokers with and without lung cancer. BMI was compared with other popular filter-based feature selection methods on both data set and showed competitive performance in selecting useful features for various classification algorithms. Since of the latter data set includes information regarding specific genes whose tissue differentiation relevance has been validated by quantitative RT-PCR, we also compared how these genes were ranked by different feature selection algorithm. The validated genes generally were assigned higher ranks by BMI than by other methods, implying that BMI should be effective in identifying biomarkers that show differential expression in cancerous samples. We also compared BMI with the approach in the original analysis conducted on the lung cancer microarray data  by contrasting the classification performance using selected genes from each method. Given models trained for various classification algorithms, classifiers based on genes selected by BMI showed better performance than those from original study. Finally, in evaluating whether the genes selected by BMI have known biological function related to (lung) cancer, we analyzed their pathway disposition and found that many genes were associated with known cancer-related pathways. Thus we can conclude that BMI is a suitable technique for phenotypic classification of microarray data and may provide a reasonable mechanism for identifying viable diagnostic biomarker candidates. Based on the results in this study, we are pursuing a follow-up study using BMI to identify biomarkers suitable for the lung cancer analysis with experimental data on clinically derived tissues.
This publication was made possible by grant number P20 RR016475 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). We also would like to thank Drs. Michael Netzer and Christian Baumgartner from University of Health Sciences, Medical Informatics and Technology (UMIT), Austria in providing source code for BMI implementation.
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