- Research article
- Open Access
A novel method for gathering and prioritizing disease candidate genes based on construction of a set of disease-related MeSH® terms
© Ono and Kuhara; licensee BioMed Central Ltd. 2014
- Received: 12 November 2013
- Accepted: 2 June 2014
- Published: 10 June 2014
Understanding the molecular mechanisms involved in disease is critical for the development of more effective and individualized strategies for prevention and treatment. The amount of disease-related literature, including new genetic information on the molecular mechanisms of disease, is rapidly increasing. Extracting beneficial information from literature can be facilitated by computational methods such as the knowledge-discovery approach. Several methods for mining gene-disease relationships using computational methods have been developed, however, there has been a lack of research evaluating specific disease candidate genes.
We present a novel method for gathering and prioritizing specific disease candidate genes. Our approach involved the construction of a set of Medical Subject Headings (MeSH) terms for the effective retrieval of publications related to a disease candidate gene. Information regarding the relationships between genes and publications was obtained from the gene2pubmed database. The set of genes was prioritized using a “weighted literature score” based on the number of publications and weighted by the number of genes occurring in a publication. Using our method for the disease states of pain and Alzheimer’s disease, a total of 1101 pain candidate genes and 2810 Alzheimer’s disease candidate genes were gathered and prioritized. The precision was 0.30 and the recall was 0.89 in the case study of pain. The precision was 0.04 and the recall was 0.6 in the case study of Alzheimer’s disease. The precision-recall curve indicated that the performance of our method was superior to that of other publicly available tools.
Our method, which involved the use of a set of MeSH terms related to disease candidate genes and a novel weighted literature score, improved the accuracy of gathering and prioritizing candidate genes by focusing on a specific disease.
- MeSH Term
- Gene Prioritization
- Disease Candidate Gene
- Cosine Similarity Measure
Understanding the molecular mechanisms involved in disease is critical for the development of more effective and individualized strategies for prevention and treatment. At present, there are several strategies available for gathering appropriate information about the molecular mechanisms of disease from a genetic point of view. One of these strategies is to search specific disease-related gene databases [1, 2]. As these databases are built based on manual processes, the data quality is high. However, owing to high manpower costs, it is difficult to maintain these databases with the large volume of ever-growing new literatures.
The other strategy is to use bioinformatics methods to extract and prioritize disease candidate genes automatically [3, 4]. These methods have been classified into several categories, such as text mining and integration of multiple data sources. Text mining methods have been particularly well studied in the biological field, because scientific literature represents a rich source for mining-based retrieval of information on gene-disease relationships. Some methods for extracting knowledge from literature are based on keyword co-occurrence analysis and the automatic extraction of entity names from text . The ranking method of gene prioritization is based on the co-occurrence of query terms, association words, and database terms, and a rule-based pattern recognition algorithm. Examples of these tools include PolySearch  and LEGENDA . In addition, methods to extract and prioritize candidate genes based on multiple data sources, such as sequence-based features, annotation data and GWAS data, have been proposed. Examples of these tools include Genotator  and Gene Prospector . While several attempts have been made to comprehensively extract and prioritize candidate disease genes by using bioinformatics techniques, a methodology for determining specific disease-relevant genes, such as pain, has not yet been fully developed .
The aim of our study was to develop a semi-automated method of gathering and prioritization of specific disease-related genes using a specialist’s knowledge that is GO and MP term selection. In this study, our approach has been applied to pain disease. In addition, we conducted a gene search related to Alzheimer’s disease (AD) to evaluate the application of this method to other specific disease. There are significant unmet medical needs in both diseases. To understand the underlying molecular mechanism is important to develop the new treatment and drug.
Our method involved the following: avoiding errors associated with gene name recognition using the gene2pubmed database , which links to PubMed® literature related to the gene, improving information retrieval from PubMed by creating a set of pain-related MeSH terms, and improving the prioritization accuracy with a novel score based on the number of publications. The priority score is weighted by the number of genes occurring in a publication. The performance of our method was compared to those of other publicly available tools. We will illustrate our method and present the results of its performance.
Literature data available in July 2012 was obtained from the NLM (National Library of Medicine). MeSH terms were also obtained from NLM (http://www.nlm.nih.gov/mesh/meshhome.html). GO terms  were downloaded from the Gene Ontology Consortium web site (http://www.geneontology.org/). Mammalian phenotype (MP) terms  were downloaded from the Mouse Genome Informatics (MGI) website (http://www.informatics.jax.org/searches/MP_form.shtml). The list of pain-related genes was downloaded from the Pain Gene Database website (http://www.jbldesign.com/jmogil/enter.html) . The list of AD-related genes was constructed from OMIM and KEGG database [15, 16].
Two sets of disease-related genes were generated to assess the performance of the method for each disease, those were pain and AD. The first set, gene set 1, was used to assess the performance of the disease-related MeSH terms and prioritizing score. The other set, gene set 2, was used to compare the performance of our method to a simple approach based on the number of the gene-related publications, resulting from the search keyword, for example, “pain” or “pain [MeSH]”, as well as with other publicly available tools.
Lists of a) gene ontology terms and b) mammalian phenotype terms that were used to create pain gene set 1
Sensory perception of pain
Detection of chemical stimulus involved in sensory perception of pain
Detection of electrical stimulus involved in sensory perception of pain
Detection of mechanical stimulus involved in sensory perception of pain
Detection of temperature stimulus involved in sensory perception of pain
Regulation of sensory perception of pain
Modulation of sensory perception of pain in another organism
Sensory perception of fast pain
Sensory perception of slow pain
Response to pain
Behavioral response to pain
Behavioral response to chemical pain
Behavioral response to acetic acid induced pain
Behavioral response to formalin induced pain
Unresponsive to tactile stimuli
Abnormal pain threshold
Increased thermal nociceptive threshold
Abnormal chemically-elicited antinociception
Increased chemically-elicited antinociception
Decreased chemically-elicited antinociception
Abnormal thermal nociception
Abnormal mechanical nociception
Abnormal chemical nociception
Abnormal nociception after inflammation
Hyperresponsive to tactile stimuli
Decreased thermal nociceptive threshold
Abnormal response to tactile stimuli
Hyporesponsive to tactile stimuli
Increased chemical nociceptive threshold
Decreased chemical nociceptive threshold
Lists of a) gene ontology terms and b) mammalian phenotype terms that were used to create AD gene set 1
Slet amyloid polypeptide processing
Amyloid precursor protein metabolic process
Amyloid precursor protein biosynthetic process
Regulation of amyloid precursor protein biosynthetic process
Amyloid precursor protein catabolic process
S100 protein binding
S100 beta biosynthetic process
S100 alpha biosynthetic process
Tau protein binding
Beta-amyloid metabolic process
Regulation of beta-amyloid clearance
Regulation of beta-amyloid formation
Amyloid fibril formation
Alpha-synuclein inclusion body
Tau protein deposits
Overview of the method for the gathering and prioritizing of disease candidate genes
Obtaining of the relationship between genes and publications
The relationship between genes and publications was collected with gene2pubmed databases. The gene2pubmed database contains curated associations between the NCBI Gene and PubMed databases. Gene2pubmed database links to publications for each gene and is not limited to articles specifically addressing the function of gene. We retrieved gene information from publications resulting from a search for disease-related MeSH terms.
We investigated orthologous gene pairs using the Homologene database  to unify the redundancy of genes for multiple species. In this study, genes from human, mouse, and rat species were considered, because the majority of studies in the field of pain and AD research is conducted in these species.
Selection of disease-related MeSH terms
To achieve comprehensive retrieval of publications related to a disease candidate gene, we constructed an optimal set of MeSH terms by calculating the frequency of co-occurrence between the MeSH terms for the disease states of “pain” or “Alzheimer disease”, and other MeSH terms.
The occurrence similarity between these terms in publications which were referred in the gene2pubmed database was calculated using cosine similarity, Dice similarity, Jaccard similarity, mutual information, and Simpson similarity measures.
Where |X| refers to the number of publications with the MeSH term for the disease and |Y| refers to the number of publications with another MeSH term. |X ∩ Y| refers to the number of publications with the MeSH term for the disease co-occurring with another MeSH term. P(X,Y) is the probability that X and Y elements appear at the same time. P(X) and P(Y) are the probabilities of occurrence of each element.
Example of pain-related MeSH terms obtained on the basis of the cosine similarity
MeSH term set
C, F, G
Posterior horn cells
The relationships between genes and publications were obtained using the method previously described. The accuracy of the obtained gene list was evaluated using recall at rank which was the number of genes obtained in publications using the query “pain [MeSH:NoExp]” or “Alzheimer Disease [MeSH:NoExp]”. The set of MeSH terms that achieved the highest recall was defined as the set of “pain-related MeSH terms” or “AD-related MeSH terms”.
Calculation of the prioritizing score
Where n refers to the total number of publications associated with the gene2pubmed database, and Pj refers to the number of genes associated with publication j. f(i, j) = 0 if gene i is not associated with publication j and f(i, j) = 1 if gene i is associated with publication j.
To assess the performance of this scoring method, we compared it against three other well-known scoring methods based on the number of gene-related publications. The measures used for comparison were the number of publications, modified TF-IDF measure, and p-value calculated with the hypergeometric distribution and Benjamini-Hochberg false discovery rate correction .
Lj refers to the number of publication associated with gene i.
The recall of each rank of genes from each scoring method was calculated against gene set 1. The Wilcoxon signed-rank test was used to calculate the statistical significance of prioritization.
Performance assessment of gene prioritization
To assess the performance of gene prioritization, we calculated the accumulated precision, recall, and F-measure for the top n out of the total genes in the ranking. In this approach, Tn represents the number of genes retrieved by our method or other publicly available tools that have been extracted correctly in the top n genes, which were included in gene set 2. C is the total number of genes in gene set 1 or gene set 2. En is the number of genes extracted by our method or other publicly available tools in the top n genes.
The maximum F-measure was also used to compare to performance of gene prioritization.
Comparing the performance against other keywords
We compared the performance of our method to a simple approach based on the ranking of the genes according to the number of gene related publications, resulting from the search term “pain” or “pain [MeSH]” in the case study of pain. First, we retrieved publications from PubMed using the keyword “pain” or “pain [MeSH]”. Next, the relationships between these publications and genes were obtained from the gene2pubmed database. Then, a prioritizing score was calculated from the number the gene related publications. Finally, for each method we compared the values of accumulated precision, recall, and maximum F-measure for the top n out of the total genes in the ranking. We also conducted this comparison for AD.
Comparing the performance against other publicly available tools
We compared the performance of our method against several publicly available tools which extract the general gene-disease relationship by using various methods, which are text mining and integration of multiple data sources, in order to assess the effect of focusing on pain field. PolySearch and LEGENDA extract knowledge data from the literature based on keyword co-occurrence analysis and automatic extraction of entity names from text. Genotator and Gene Prospector extract and prioritize candidate genes based on multiple data sources.
The prioritization lists of pain or AD candidate genes identified using other tools were compiled using queries of the keyword “pain” or “Alzheimer’s disease”, and default parameters as of September 2012. In PolySearch, genes with the description “protein family or complex” were excluded because it was not possible to determine the relationships between genes and gene symbols within the NCBI Gene database. As these tools are limited to human genes, orthologous information was incorporated by the Homologene database. We compared the value of the accumulated precision, recall, and maximum F-measure for the top n out of the total genes in the ranking.
Case study 1: pain
Pain is a major healthcare issue as defined by the World Health Organization and has complex pathophysiology [23, 24]. Especially, chronic pain has remained a major healthcare issue affecting not only patients by decreasing their quality of life but also society as a whole by increasing socioeconomic costs. Unfortunately, many pathological pain conditions remain poorly understood and resist currently available treatment. Therefore, the development of new therapeutic approaches to managing pain will undoubtedly depend on a better understanding of the molecular, cellular, and circuit mechanisms underlying pain states.
In this study, genes related to primary disease, such as diabetes mellitus, cancer, and infectious disease were not considered.
Evaluation of scoring methods for gene prioritization
Therefore, for subsequent analyses, the weighted literature score was applied for prioritization.
Selection of pain-related MeSH terms
Table 3 shows that the example of MeSH terms with a high occurrence similarity with the MeSH term “pain” calculated by the cosine similarity and the recall of gathering genes. MeSH terms with close cosine distance to the MeSH term “pain” belonged to various categories of MeSH tree structures (Table 3). Some of these categories are different from the categories that the MeSH term “pain” belongs to, which are “C” (Disease), “F” (Psychiatry and Psychology), and “G” (Phenomena and Processes). The MeSH term with the closest cosine distance value (0.34) was “Pain Measurement” which belongs to category “E” (Analytical, Diagnostic, and Therapeutic Techniques and Equipment). The term with the second closest cosine distance value (0.268) was “Nociceptors” which belongs to category “A” (Anatomy).
Gathering and prioritizing the pain candidate genes
The top-20 ranked pain candidate genes gathered by our method
Transient receptor potential cation channel, subfamily V, member 1
Opioid receptor, mu 1
Transient receptor potential cation channel, subfamily A, member 1
Tachykinin receptor 1
Purinergic receptor P2X, ligand-gated ion channel, 3
Brain-derived neurotrophic factor
Sodium channel, voltage-gated, type IX, alpha
Prostaglandin-endoperoxide synthase 2
Cannabinoid receptor 1 (brain)
Nerve growth factor (beta polypeptide)
Tumor necrosis factor
Acid-sensing (proton-gated) ion channel 3
Sodium channel, voltage-gated, type X, alpha subunit
Tachykinin, precursor 1
FBJ osteosarcoma oncogene
Calcitonin-related polypeptide alpha
Glutamate receptor, ionotropic, N-methyl D-aspartate 1
Comparison with other tools
Summary of the maximum F-measures for pain candidate genes from our method and those from publicly available tools
# of total gene
Rank at Max. F-measure
One-hundred and sixty of 381 genes which were the number of genes at the rank of maximum F-measure were not extracted by other publicly available tools. Of these 160 genes, 94 were included in the pain gene set 2 (see Additional file 2). Acid-sensing ion channel 3 (ASIC3) which ranked at 13 (Table 4) is a typical example. ASIC3 is the most sensitive acid sensor in sensory neurons, and secondary mechanical hyperalgesia is not observed in knockout mice for this gene . This channel is critical for the development of secondary hyperalgesia as measured by mechanical stimulation of the paw following muscle insult. Another example is the gene encoding L1 cell adhesion molecule, which was also identified solely by our method (ranked at 162, Additional file 1). This gene encodes a cell adhesion molecule that contributes to axonal outgrowth, guidance, and fasciculation in development, in addition to synapse formation and plasticity. This gene plays a role in the maintenance of thermal hyperalgesia following spinal cord injury in mice . These results suggest that our method is more effective for the comprehensive gathering of pain candidate genes than publicly available tools.
Case 2: Alzheimer’s disease
In order to evaluate the application of this method to other diseases, we conducted a gene search for AD. There is a clear and significant need for better therapy for AD. It is critical to understand the underlying molecular mechanism of AD for the development of novel treatments.
Evaluation of scoring methods for gene prioritization
We evaluated the performance of scoring methods for gene prioritization for AD as we did in the case of pain. A total of 2178 genes were obtained from publications retrieved from a search using the MeSH term “Alzheimer Disease [Mesh:NoExp]” in PubMed. The prioritization scores of these genes were calculated using four methods. The recall of each method is shown in Figure 2B. The weighted literature score produced the best performance (p < .05). The higher ranked genes were predicted accurately with each method. The weighted literature score achieved better prediction accuracy with low ranking genes than that of other methods.
Selection of AD-related MeSH terms
Figure 3 shows the recall of genes obtained from publications retrieved from searches for each set of MeSH terms using various similarity measures. The highest recall (0.886) was achieved using MeSH term set 6, which was constructed using MeSH term similarity calculated by the cosine similarity measure. This set comprised the combination of the MeSH terms “Alzheimer Disease”, “Amyloid beta-Peptides”, “Amyloid beta-Protein Precursor”, “Presenilin-1”, “Apolipoprotein E4”, “Plaque, Amyloid”, and “tau Proteins”. These seven MeSH terms were defined as AD-related MeSH terms.
Gathering and prioritizing AD candidate genes
To assess the performance of our method, precision and recall for three gene sets were compared with AD gene set 2 at each gene rank. These sets were created using publications resulting from searches for AD-related MeSH terms, “Alzheimer’s disease” and “Alzheimer disease [MeSH]” in Pubmed.
The top-20 ranked AD candidate genes gathered by our method
Amyloid beta (A4) precursor protein
Microtubule-associated protein tau
Beta-site APP cleaving enzyme 1
Synuclein, alpha (non A4 component of amyloid precursor)
Glycogen synthase kinase 3 beta
Brain-derived neurotrophic factor
Amyloid beta (A4) precursor-like protein 2
Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2
Insulin degrading enzyme
Cyclin-dependent kinase 5
Sortilin-related receptor, LDLR class A repeats-containing
Angiotensin I converting enzyme
Amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)
The precision and recall values for 2940 genes from simple approach based on the ranking of the genes by the number of times the gene appears with keyword “Alzheimer’s Disease” were 0.04 and 0.63, respectively, whereas the precision and recall values for 2178 genes from simple approach with using the keyword “Alzheimer’s Disease [MeSH]” were 0.04 and 0.53, respectively. The maximum F-measures for AD-related MeSH terms, “Alzheimer’s Disease” and “Alzheimer Disease [MeSH]” were 0.24, 0.22, and 0.23 with gene ranks of 166, 134, and 194, respectively.
Comparison with other tools
Summary of the maximum F-measures for AD candidate genes from our method and those from publicly available tools
# of total gene
Rank at Max. F-measure
Two of 166 genes which were the number of genes at the rank of maximum F-measure were not extracted by other publicly available tools and were not included in AD gene set 2. These two genes were chemokine (C-X3-C motif) receptor 1 (CX3CR1) and Bcl2-associated X protein (BAX). Nonetheless, there are publications that provide evidence for an association between these genes and AD. CX3CR1, which ranked 132, is a key microglial pathway in protecting against AD-related cognitive deficits that are associated with aberrant microglial activation and elevated inflammatory cytokines . BAX, which ranked 164, plays a role in neuronal cell death. Importantly, expression levels of these proteins are reportedly altered in vulnerable neurons in AD. The inhibition of Bax activity using either Bax-inhibiting peptide or Bax gene knockout significantly prevented oligomeric amyloid beta-induced neuronal cell death .
While several attempts have been made to develop methods for extracting and prioritizing disease candidate genes using bioinformatics techniques, a methodology for the inference of specific disease-relevant genes, such as pain or AD, has not yet been developed . In this study, we developed computational methods to gather and prioritize the most likely candidate genes associated with specific disease. The features of our method include creating a set of disease related MeSH terms for the comprehensive retrieval of disease candidate gene related publications, and developing a novel prioritization score for improving ranking accuracy. The relationships between genes and publications were correctly obtained using the gene2pubmed database. There are other sources to find relationships between genes and publications such as Gene Reference Into Function (GeneRIF), which uses the gene-disease relation extraction system . GeneRIF is a database in which human experts provide a brief summary of gene functions and make the connections between citations (PubMed) and NCBI Gene databases . Although we used this index to obtain a relationship between genes and publications, we could not obtain a good performance (data not shown). Many methods for extracting knowledge from the literature using text mining are based on co-occurrence analysis of given keywords, which automatically extracts entity names from the text. However, automatic entity name recognition methods often incorrectly identify a significant portion of genes mentioned within the text [31, 32] and consequently introduce noise and ambiguity into the extraction method. For example, in the case study of pain, the word TENS was recognized as a gene name by PolySearch and LEGENDA. However, in the field of pain research, TENS is usually used as an abbreviation for “transcutaneous electrical nerve stimulation”, a therapeutic strategy. To avoid this problem, our method used the gene2pubmed database which contains a list of associations between PubMed IDs and unambiguous gene identifiers.
By focusing on specific disease, we assembled disease-related MeSH terms to improve information retrieval from PubMed. In the case study of pain, a best set of MeSH terms, including “pain”, “pain measurement”, “nociceptor”, “pain threshold”, and “hyperalgesia”, was selected with the highest recall for pain gene set 1. Recall was reduced when MeSH terms (excluding pain-related MeSH terms) which appeared as frequently as “pain” (i.e., “posterior horn cells”, “ganglia, spinal”, “injections, spinal”, “physical stimulation”, and “formaldehyde”), were added to the set in the case of cosine similarity measure. This may be because these terms do not have a specific meaning for pain disease. “Posterior horn cells” and “ganglia, spinal” refer to tissue, while “injections, spinal” and “physical stimulation” refer to general methods, and “formaldehyde” identifies the general reagent. So, the genes that were not related to pain were extracted using these MeSH terms. Because pain-related MeSH terms belong to various MeSH categories, comprehensive gathering was achieved, which could not be accomplished by searching only the MeSH term “pain”. The example is the gene that encodes reticulon 4 (Rtn4), which was referenced in publications by the MeSH term “pain measurement”. This gene was assigned to GO term “GO: 0051930 regulation of sensory perception of pain”. The related publication indicated that Nogo-66, the 66-residue domain of Rtn4, may be related to a reduction in neuropathic pain following periphery nerve injury .
In the top-ranked 381 genes, 94 genes were not extracted by the other publicly available tools from the pain gene set 2; in addition, 121 pain candidate genes were not included in both pain gene set 1 and 2. An example of these 121 genes is FBJ murine osteosarcoma viral oncogene homolog (FOS) which ranked at 16, this has been extensively used as a marker for the activation of nociceptive neurons in the spinal cord . The degree of spinal c-Fos expression was correlated with the extent of the pain-related behavior of carrageenan-injected rats . Another example is sphingosine-1-phosphate receptor 1 gene (S1PR1) which ranked at 196. Sphingosine-1-phosphate (S1P) is a key regulator of the immune response. S1P- and inflammation-induced hypersensitivity is significantly reduced in mice with a conditional nociceptor-specific deletion in S1PR1. Thus, S1P/S1PR1 signaling may be a key player in the onset of thermal hypersensitivity and hyperalgesia. These results suggest that our method was very effective for the comprehensive gathering of pain candidate genes.
To achieve high prioritization accuracy, we defined a weighted literature score. Several conventional methods have been used to calculate the co-occurrence frequency and appearance for the prioritization of each gene. Other text mining methods use the statistical p-value calculated from the number of publications . However, the prioritization scores from these methods are likely to be overestimated, because several publications related to –omics analysis, such as microarray and genome sequence analysis, may cite many genes. We hypothesized that the contribution of these studies to each gene is relatively minor, and developed the weighted literature score to account for the number of genes studied in a given publication. The results of our study indicate that weighted literature scores improved performance compared with other scoring methods.
The results of our AD case study illustrate the applicability of our method to other diseases. However, the limitation is the lack of comprehensive applicability to other diseases. Disease-specific systems are able to exploit domain knowledge more thoroughly and thus achieve higher accuracy than general purpose systems, but the utility of these systems is not portable . Our method is a semi-automated method for which a specialist’s knowledge is needed for GO and MP term selection. It is expected that adaptation to other diseases can also be promoted in the future if the retrieval of disease specific MeSH terms can be performed efficiently and automatically.
Another limitation of our method is that it will not discover novel disease candidate genes that are not cited in the disease-related literature. This includes studies that are newly registered in PubMed for which there would be no gene-PubMed ID relationship in GeneRIF or gene2pubmed and no MeSH term information. However, the accumulation of precise information from the literature by using our method may help to advance our understanding of disease mechanisms. It may also lead to the generation of novel hypotheses for understanding molecular mechanisms involved in disease when used in combination with further analyses such as network analysis . We believe that our method for the comprehensive retrieval of disease candidate genes from the literature is a useful step toward understanding the mechanisms of disease.
Our method, which involves the use of a set of disease-related MeSH terms and a weighted literature score, showed better performance than did other publicly available tools that extract general gene-disease associations.
The gene list obtained with our method would be beneficial for the study of disease mechanisms and would also provide a source of potential disease biomarkers and potential targets for novel therapies.
We thank Haretsugu Hishigaki for comments and discussion on the research. Our research was supported by both the Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University and Otsuka Pharmaceutical Co. Ltd.
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