Mining for novel tumor suppressor genes using a shortest path approach

Inferring novel genes related to colorectal cancer via random walk with restart algorithm

Colorectal cancer (CRC) is the third most common type of cancer. In recent decades, genomic analysis has played an increasingly important role in understanding the molecular mechanisms of CRC. However, its pathogenesis has not been fully uncovered. Identification of genes related to CRC as complete as possible is an important way to investigate its pathogenesis. Therefore, we proposed a new computational method for the identification of novel CRC-associated genes. The proposed method is based on existing proven CRC-associated genes, human protein-protein interaction networks, and random walk with restart algorithm. The utility of the method is indicated by comparing it to the methods based on Guilt-by-association or shortest path algorithm. Using the proposed method, we successfully identified 298 novel CRC-associated genes. Previous studies have validated the involvement of the majority of these 298 novel genes in CRC-associated biological processes, thus suggesting the efficacy and accuracy of our method.

A Binary Classifier for the Prediction of EC Numbers of Enzymes

Background:

Identification of Enzyme Commission (EC) number of enzymes is quite important for understanding the metabolic processes that produce enough energy to sustain life. Previous studies mainly focused on predicting six main functional classes or sub-functional classes, i.e., the first two digits of the EC number.

Objective:

In this study, a binary classifier was proposed to identify the full EC number (four digits) of enzymes.

Methods:

Enzymes and their known EC numbers were paired as positive samples and negative samples were randomly produced that were as many as positive samples. The associations between any two samples were evaluated by integrating the linkages between enzymes and EC numbers. The classic machining learning algorithm, Support Vector Machine (SVM), was adopted as the prediction engine.

Results:

The five-fold cross-validation test on five datasets indicated that the overall accuracy, Matthews correlation coefficient and F1-measure were about 0.786, 0.576 and 0.771, respectively, suggesting the utility of the proposed classifier. In addition, the effectiveness of the classifier was elaborated by comparing it with other classifiers that were based on other classic machine learning algorithms.

Conclusion:

The proposed classifier was quite effective for prediction of EC number of enzymes and was specially designed for dealing with the problem addressed in this study by testing it on five datasets containing randomly produced samples.

Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links

BACKGROUND

Netpredictor is an R package for prediction of missing links in any given unipartite or bipartite network. The package provides utilities to compute missing links in a bipartite and well as unipartite networks using Random Walk with Restart and Network inference algorithm and a combination of both. The package also allows computation of Bipartite network properties, visualization of communities for two different sets of nodes, and calculation of significant interactions between two sets of nodes using permutation based testing. The application can also be used to search for top-K shortest paths between interactome and use enrichment analysis for disease, pathway and ontology. The R standalone package (including detailed introductory vignettes) and associated R Shiny web application is available under the GPL-2 Open Source license and is freely available to download.

RESULTS

We compared different algorithms performance in different small datasets and found random walk supersedes rest of the algorithms. The package is developed to perform network based prediction of unipartite and bipartite networks and use the results to understand the functionality of proteins in an interactome using enrichment analysis.

CONCLUSION

The rapid application development envrionment like shiny, helps non programmers to develop fast rich visualization apps and we beleieve it would continue to grow in future with further enhancements. We plan to update our algorithms in the package in near future and help scientist to analyse data in a much streamlined fashion.

Inferring Novel Tumor Suppressor Genes with a Protein-Protein Interaction Network and Network Diffusion Algorithms

Extensive studies on tumor suppressor genes (TSGs) are helpful to understand the pathogenesis of cancer and design effective treatments. However, identifying TSGs using traditional experiments is quite difficult and time consuming. Developing computational methods to identify possible TSGs is an alternative way. In this study, we proposed two computational methods that integrated two network diffusion algorithms, including Laplacian heat diffusion (LHD) and random walk with restart (RWR), to search possible genes in the whole network. These two computational methods were LHD-based and RWR-based methods. To increase the reliability of the putative genes, three strict screening tests followed to filter genes obtained by these two algorithms. After comparing the putative genes obtained by the two methods, we designated twelve genes (e.g., MAP3K10, RND1, and OTX2) as common genes, 29 genes (e.g., RFC2 and GUCY2F) as genes that were identified only by the LHD-based method, and 128 genes (e.g., SNAI2 and FGF4) as genes that were inferred only by the RWR-based method. Some obtained genes can be confirmed as novel TSGs according to recent publications, suggesting the utility of our two proposed methods. In addition, the reported genes in this study were quite different from those reported in a previous one.

Cross talk of chromosome instability, CpG island methylator phenotype and mismatch repair in colorectal cancer

Colorectal cancer is a severe cancer associated with a high prevalence and fatality rate. There are three major mechanisms for colorectal cancer: (1) Chromosome instability (CIN), (2) CpG island methylator phenotype (CIMP) and (3) mismatch repair (MMR), of which CIN is the most common type. However, these subtypes are not exclusive and overlap. To investigate their biological mechanisms and cross talk, the gene expression profiles of 585 colorectal cancer patients with CIN, CIMP and MMR status records were collected. By comparing the CIN+ and CIN-samples, CIMP+ and CIMP-samples, MMR+ and MMR-samples with minimal redundancy maximal relevance (mRMR) and incremental feature selection (IFS) methods, the CIN, CIMP and MMR associated genes were selected. Unfortunately, there was little direct overlap among them. To investigate their indirect interactions, downstream genes of CIN, CIMP and MMR were identified using the random walk with restart (RWR) method and a greater overlap of downstream genes was indicated. The common downstream genes were involved in biosynthetic and metabolic pathways. These findings were consistent with the clinical observation of wide range metabolite aberrations in colorectal cancer. To conclude, the present study gave a gene level explanation of CIN, CIMP and MMR, but also showed the network level cross talk of CIN, CIMP and MMR. The common genes of CIN, CIMP and MMR may be useful for cross-subtype general colorectal cancer drug development.

Deciphering the Relationship between Obesity and Various Diseases from a Network Perspective

The number of obesity cases is rapidly increasing in developed and developing countries, thereby causing significant health problems worldwide. The pathologic factors of obesity at the molecular level are not fully characterized, although the imbalance between energy intake and consumption is widely recognized as the main reason for fat accumulation. Previous studies reported that obesity can be caused by the dysfunction of genes associated with other diseases, such as myocardial infarction, hence providing new insights into dissecting the pathogenesis of obesity by investigating its associations with other diseases. In this study, we investigated the relationship between obesity and diseases from Online Mendelian Inheritance in Man (OMIM) databases on the protein–protein interaction (PPI) network. The obesity genes and genes of one OMIM disease were mapped onto the network, and the interaction scores between the two gene sets were investigated on the basis of the PPI of individual gene pairs, thereby inferring the relationship between obesity and this disease. Results suggested that diseases related to nutrition and endocrine are the top two diseases that are closely associated with obesity. This finding is consistent with our general knowledge and indicates the reliability of our obtained results. Moreover, we inferred that diseases related to psychiatric factors and bone may also be highly related to obesity because the two diseases followed the diseases related to nutrition and endocrine according to our results. Numerous obesity–disease associations were identified in the literature to confirm the relationships between obesity and the aforementioned four diseases. These new results may help understand the underlying molecular mechanisms of obesity–disease co-occurrence and provide useful insights for disease prevention and intervention.

Identification of genes related to proliferative diabetic retinopathy through RWR algorithm based on protein-protein interaction network

Proliferative diabetic retinopathy (PDR) is one of the most common complications of diabetes and can lead to blindness. Proteomic studies have provided insight into the pathogenesis of PDR and a series of PDR-related genes has been identified but are far from fully characterized because the experimental methods are expensive and time consuming. In our previous study, we successfully identified 35 candidate PDR-related genes through the shortest-path algorithm. In the current study, we developed a computational method using the random walk with restart (RWR) algorithm and the protein-protein interaction (PPI) network to identify potential PDR-related genes. After some possible genes were obtained by the RWR algorithm, a three-stage filtration strategy, which includes the permutation test, interaction test and enrichment test, was applied to exclude potential false positives caused by the structure of PPI network, the poor interaction strength, and the limited similarity on gene ontology (GO) terms and biological pathways. As a result, 36 candidate genes were discovered by the method which was different from the 35 genes reported in our previous study. A literature review showed that 21 of these 36 genes are supported by previous experiments. These findings suggest the robustness and complementary effects of both our efforts using different computational methods, thus providing an alternative method to study PDR pathogenesis.

Prediction of potential drivers connecting different dysfunctional levels in lung adenocarcinoma via a protein-protein interaction network

Lung cancer is a serious disease that threatens an affected individual's life. Its pathogenesis has not yet to be fully described, thereby impeding the development of effective treatments and preventive measures. "Cancer driver" theory considers that tumor initiation can be associated with a number of specific mutations in genes called cancer driver genes. Four omics levels, namely, (1) methylation, (2) microRNA, (3) mutation, and (4) mRNA levels, are utilized to cluster cancer driver genes. In this study, the known dysfunctional genes of these four levels were used to identify novel driver genes of lung adenocarcinoma, a subtype of lung cancer. These genes could contribute to the initiation and progression of lung adenocarcinoma in at least two levels. First, random walk with restart algorithm was performed on a protein-protein interaction (PPI) network constructed with PPI information in STRING by using known dysfunctional genes as seed nodes for each level, thereby yielding four groups of possible genes. Second, these genes were further evaluated in a test strategy to exclude false positives and select the most important ones. Finally, after conducting an intersection operation in any two groups of genes, we obtained several inferred driver genes that contributed to the initiation of lung adenocarcinoma in at least two omics levels. Several genes from these groups could be confirmed according to recently published studies. The inferred genes reported in this study were also different from those described in a previous study, suggesting that they can be used as essential supplementary data for investigations on the initiation of lung adenocarcinoma. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.

Network-Based Method for Identifying Co- Regeneration Genes in Bone, Dentin, Nerve and Vessel Tissues

Bone and dental diseases are serious public health problems. Most current clinical treatments for these diseases can produce side effects. Regeneration is a promising therapy for bone and dental diseases, yielding natural tissue recovery with few side effects. Because soft tissues inside the bone and dentin are densely populated with nerves and vessels, the study of bone and dentin regeneration should also consider the co-regeneration of nerves and vessels. In this study, a network-based method to identify co-regeneration genes for bone, dentin, nerve and vessel was constructed based on an extensive network of protein–protein interactions. Three procedures were applied in the network-based method. The first procedure, searching, sought the shortest paths connecting regeneration genes of one tissue type with regeneration genes of other tissues, thereby extracting possible co-regeneration genes. The second procedure, testing, employed a permutation test to evaluate whether possible genes were false discoveries; these genes were excluded by the testing procedure. The last procedure, screening, employed two rules, the betweenness ratio rule and interaction score rule, to select the most essential genes. A total of seventeen genes were inferred by the method, which were deemed to contribute to co-regeneration of at least two tissues. All these seventeen genes were extensively discussed to validate the utility of the method.

A computational method using the random walk with restart algorithm for identifying novel epigenetic factors

Epigenetic regulation has long been recognized as a significant factor in various biological processes, such as development, transcriptional regulation, spermatogenesis, and chromosome stabilization. Epigenetic alterations lead to many human diseases, including cancer, depression, autism, and immune system defects. Although efforts have been made to identify epigenetic regulators, it remains a challenge to systematically uncover all the components of the epigenetic regulation in the genome level using experimental approaches. The advances of constructing protein-protein interaction (PPI) networks provide an excellent opportunity to identify novel epigenetic factors computationally in the genome level. In this study, we identified potential epigenetic factors by using a computational method that applied the random walk with restart (RWR) algorithm on a protein-protein interaction (PPI) network using reported epigenetic factors as seed nodes. False positives were identified by their specific roles in the PPI network or by a low-confidence interaction and a weak functional relationship with epigenetic regulators. After filtering out the false positives, 26 candidate epigenetic factors were finally accessed. According to previous studies, 22 of these are thought to be involved in epigenetic regulation, suggesting the robustness of our method. Our study provides a novel computational approach which successfully identified 26 potential epigenetic factors, paving the way on deepening our understandings on the epigenetic mechanism.

A network-based method using a random walk with restart algorithm and screening tests to identify novel genes associated with Menière's disease

As a chronic illness derived from hair cells of the inner ear, Menière’s disease (MD) negatively influences the quality of life of individuals and leads to a number of symptoms, such as dizziness, temporary hearing loss, and tinnitus. The complete identification of novel genes related to MD would help elucidate its underlying pathological mechanisms and improve its diagnosis and treatment. In this study, a network-based method was developed to identify novel MD-related genes based on known MD-related genes. A human protein-protein interaction (PPI) network was constructed using the PPI information reported in the STRING database. A classic ranking algorithm, the random walk with restart (RWR) algorithm, was employed to search for novel genes using known genes as seed nodes. To make the identified genes more reliable, a series of screening tests, including a permutation test, an interaction test and an enrichment test, were designed to select essential genes from those obtained by the RWR algorithm. As a result, several inferred genes, such as CD4, NOTCH2 and IL6, were discovered. Finally, a detailed biological analysis was performed on fifteen of the important inferred genes, which indicated their strong associations with MD.

Determination of Genes Related to Uveitis by Utilization of the Random Walk with Restart Algorithm on a Protein-Protein Interaction Network

Uveitis, defined as inflammation of the uveal tract, may cause blindness in both young and middle-aged people. Approximately 10–15% of blindness in the West is caused by uveitis. Therefore, a comprehensive investigation to determine the disease pathogenesis is urgent, as it will thus be possible to design effective treatments. Identification of the disease genes that cause uveitis is an important requirement to achieve this goal. To begin to answer this question, in this study, a computational method was proposed to identify novel uveitis-related genes. This method was executed on a large protein–protein interaction network and employed a popular ranking algorithm, the Random Walk with Restart (RWR) algorithm. To improve the utility of the method, a permutation test and a procedure for selecting core genes were added, which helped to exclude false discoveries and select the most important candidate genes. The five-fold cross-validation was adopted to evaluate the method, yielding the average F1-measure of 0.189. In addition, we compared our method with a classic GBA-based method to further indicate its utility. Based on our method, 56 putative genes were chosen for further assessment. We have determined that several of these genes (e.g., CCL4, Jun, and MMP9) are likely to be important for the pathogenesis of uveitis.

Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm

Fruit is essential for plant reproduction and is responsible for protection and dispersal of seeds. The development and maturation of fruit is tightly regulated by numerous genetic factors that respond to environmental and internal stimulation. In this study, we attempted to identify novel fruit-related genes in a model organism, Arabidopsis thaliana, using a computational method. Based on validated fruit-related genes, the random walk with restart (RWR) algorithm was applied on a protein-protein interaction (PPI) network using these genes as seeds. The identified genes with high probabilities were filtered by the permutation test and linkage tests. In the permutation test, the genes that were selected due to the structure of the PPI network were discarded. In the linkage tests, the importance of each candidate gene was measured from two aspects: (1) its functional associations with validated genes and (2) its similarity with validated genes on gene ontology (GO) terms and KEGG pathways. Finally, 255 inferred genes were obtained, subsequent extensive analysis of important genes revealed that they mainly contribute to ubiquitination (UBQ9, UBQ8, UBQ11, UBQ10), serine hydroxymethyl transfer (SHM7, SHM5, SHM6) or glycol-metabolism (HXKL2_ARATH, CSY5, GAPCP1), suggesting essential roles during the development and maturation of fruit in Arabidopsis thaliana.

An integrated method for the identification of novel genes related to oral cancer

Cancer is a significant public health problem worldwide. Complete identification of genes related to one type of cancer facilitates earlier diagnosis and effective treatments. In this study, two widely used algorithms, the random walk with restart algorithm and the shortest path algorithm, were adopted to construct two parameterized computational methods, namely, an RWR-based method and an SP-based method; based on these methods, an integrated method was constructed for identifying novel disease genes. To validate the utility of the integrated method, data for oral cancer were used, on which the RWR-based and SP-based methods were trained, thereby building two optimal methods. The integrated method combining these optimal methods was further adopted to identify the novel genes of oral cancer. As a result, 85 novel genes were inferred, among which eleven genes (e.g., MYD88, FGFR2, NF-κBIA) were identified by both the RWR-based and SP-based methods, 70 genes (e.g., BMP4, IFNG, KITLG) were discovered only by the RWR-based method and four genes (L1R1, MCM6, NOG and CXCR3) were predicted only by the SP-based method. Extensive analyses indicate that several novel genes have strong associations with cancers, indicating the effectiveness of the integrated method for identifying disease genes.

Identifying and Analyzing Novel Epilepsy-Related Genes Using Random Walk with Restart Algorithm

As a pathological condition, epilepsy is caused by abnormal neuronal discharge in brain which will temporarily disrupt the cerebral functions. Epilepsy is a chronic disease which occurs in all ages and would seriously affect patients' personal lives. Thus, it is highly required to develop effective medicines or instruments to treat the disease. Identifying epilepsy-related genes is essential in order to understand and treat the disease because the corresponding proteins encoded by the epilepsy-related genes are candidates of the potential drug targets. In this study, a pioneering computational workflow was proposed to predict novel epilepsy-related genes using the random walk with restart (RWR) algorithm. As reported in the literature RWR algorithm often produces a number of false positive genes, and in this study a permutation test and functional association tests were implemented to filter the genes identified by RWR algorithm, which greatly reduce the number of suspected genes and result in only thirty-three novel epilepsy genes. Finally, these novel genes were analyzed based upon some recently published literatures. Our findings implicate that all novel genes were closely related to epilepsy. It is believed that the proposed workflow can also be applied to identify genes related to other diseases and deepen our understanding of the mechanisms of these diseases.

A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana

Biologically, fruits are defined as seed-bearing reproductive structures in angiosperms that develop from the ovary. The fertilization, development and maturation of fruits are crucial for plant reproduction and are precisely regulated by intrinsic genetic regulatory factors. In this study, we used Arabidopsis thaliana as a model organism and attempted to identify novel genes related to fruit-associated biological processes. Specifically, using validated genes, we applied a shortest-path-based method to identify several novel genes in a large network constructed using the protein-protein interactions observed in Arabidopsis thaliana. The described analyses indicate that several of the discovered genes are associated with fruit fertilization, development and maturation in Arabidopsis thaliana.

Identification of novel candidate drivers connecting different dysfunctional levels for lung adenocarcinoma using protein-protein interactions and a shortest path approach

Tumors are formed by the abnormal proliferation of somatic cells with disordered growth regulation under the influence of tumorigenic factors. Recently, the theory of “cancer drivers” connects tumor initiation with several specific mutations in the so-called cancer driver genes. According to the differentiation of four basic levels between tumor and adjacent normal tissues, the cancer drivers can be divided into the following: (1) Methylation level, (2) microRNA level, (3) mutation level, and (4) mRNA level. In this study, a computational method is proposed to identify novel lung adenocarcinoma drivers based on dysfunctional genes on the methylation, microRNA, mutation and mRNA levels. First, a large network was constructed using protein-protein interactions. Next, we searched all of the shortest paths connecting dysfunctional genes on different levels and extracted new candidate genes lying on these paths. Finally, the obtained candidate genes were filtered by a permutation test and an additional strict selection procedure involving a betweenness ratio and an interaction score. Several candidate genes remained, which are deemed to be related to two different levels of cancer. The analyses confirmed our assertions that some have the potential to contribute to the tumorigenesis process on multiple levels.

Investigation of the roles of trace elements during hepatitis C virus infection using protein-protein interactions and a shortest path algorithm

BACKGROUND

Hepatitis is a type of infectious disease that induces inflammation of the liver without pinpointing a particular pathogen or pathogenesis. Type C hepatitis, as a type of hepatitis, has been reported to induce cirrhosis and hepatocellular carcinoma within a very short amount of time. It is a great threat to human health. Some studies have revealed that trace elements are associated with infection with and immune rejection against hepatitis C virus (HCV). However, the mechanism underlying this phenomenon is still unclear.

METHODS

In this study, we aimed to expand our knowledge of this phenomenon by designing a computational method to identify genes that may be related to both HCV and trace element metabolic processes. The searching procedure included three stages. First, a shortest path algorithm was applied to a large network, constructed by protein-protein interactions, to identify potential genes of interest. Second, a permutation test was executed to exclude false discoveries. Finally, some rules based on the betweenness and associations between candidate genes and HCV and trace elements were built to select core genes among the remaining genes.

RESULTS

12 lists of genes, corresponding to 12 types of trace elements, were obtained. These genes are deemed to be associated with HCV infection and trace elements metabolism.

CONCLUSIONS

The analyses indicate that some genes may be related to both HCV and trace element metabolic processes, further confirming the associations between HCV and trace elements. The method was further tested on another set of HCV genes, the results indicate that this method is quite robustness.

GENERAL SIGNIFICANCE

The newly found genes may partially reveal unknown mechanisms between HCV infection and trace element metabolism. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.

The Use of Protein-Protein Interactions for the Analysis of the Associations between PM2.5 and Some Diseases

Nowadays, pollution levels are rapidly increasing all over the world. One of the most important pollutants is PM2.5. It is known that the pollution environment may cause several problems, such as greenhouse effect and acid rain. Among them, the most important problem is that pollutants can induce a number of serious diseases. Some studies have reported that PM2.5 is an important etiologic factor for lung cancer. In this study, we extensively investigate the associations between PM2.5 and 22 disease classes recommended by Goh et al., such as respiratory diseases, cardiovascular diseases, and gastrointestinal diseases. The protein-protein interactions were used to measure the linkage between disease genes and genes that have been reported to be modulated by PM2.5. The results suggest that some diseases, such as diseases related to ear, nose, and throat and gastrointestinal, nutritional, renal, and cardiovascular diseases, are influenced by PM2.5 and some evidences were provided to confirm our results. For example, a total of 18 genes related to cardiovascular diseases are identified to be closely related to PM2.5, and cardiovascular disease relevant gene DSP is significantly related to PM2.5 gene JUP.

A network-based method for the identification of putative genes related to infertility

BACKGROUND

Infertility has become one of the major health problems worldwide, with its incidence having risen markedly in recent decades. There is an urgent need to investigate the pathological mechanisms behind infertility and to design effective treatments. However, this is made difficult by the fact that various biological factors have been identified to be related to infertility, including genetic factors.

METHODS

A network-based method was established to identify new genes potentially related to infertility. A network constructed using human protein-protein interactions based on previously validated infertility-related genes enabled the identification of some novel candidate genes. These genes were then filtered by a permutation test and their functional and structural associations with infertility-related genes.

RESULTS

Our method identified 23 novel genes, which have strong functional and structural associations with previously validated infertility-related genes.

CONCLUSIONS

Substantial evidence indicates that the identified genes are strongly related to dysfunction of the four main biological processes of fertility: reproductive development and physiology, gametogenesis, meiosis and recombination, and hormone regulation.

GENERAL SIGNIFICANCE

The newly discovered genes may provide new directions for investigating infertility. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.

Mining for genes related to choroidal neovascularization based on the shortest path algorithm and protein interaction information

BACKGROUND

Choroidal neovascularization (CNV) is a serious eye disease that may cause visual loss, especially for older people. Many factors have been proven to induce this disease including age, gender, obesity, and so on. However, until now, we have had limited knowledge on CNV's pathogenic mechanism. Discovering the genes that underlie this disease and performing extensive studies on them can help us to understand how CNV occurs and design effective treatments.

METHODS

In this study, we designed a computational method to identify novel CNV-related genes in a large protein network constructed using the protein-protein interaction information in STRING. The candidate genes were first extracted from the shortest paths connecting any two known CNV-related genes and then filtered by a permutation test and using knowledge of their linkages to known CNV-related genes.

RESULTS

A list of putative CNV-related candidate genes was accessed by our method. These genes are deemed to have strong relationships with CNV.

CONCLUSIONS

Extensive analyses of several of the putative genes such as ANK1, ITGA4, CD44 and others indicate that they are related to specific biological processes involved in CNV, implying they may be novel CNV-related genes.

GENERAL SIGNIFICANCE

The newfound putative CNV-related genes may provide new insights into CNV and help design more effective treatments. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.