Abstract
Text mining methods can facilitate the generation of biomedical hypotheses by suggesting novel associations between diseases and genes. Previously, we developed a rare-term model called RaJoLink (Petric et al, J. Biomed. Inform. 42(2): 219-227, 2009) in which hypotheses are formulated on the basis of terms rarely associated with a target domain. Since many current medical hypotheses are formulated in terms of molecular entities and molecular mechanisms, here we extend the methodology to proteins and genes, using a standardized vocabulary as well as a gene/protein network model. The proposed enhanced RaJoLink rare-term model combines text mining and gene prioritization approaches. Its utility is illustrated by finding known as well as potential gene-disease associations in ovarian cancer using MEDLINE abstracts and the STRING database.
Keywords: Biomedical hypothesis generation, disease gene prediction, gene prioritization, ovarian cancer, text mining.
Protein & Peptide Letters
Title:Biomedical Hypothesis Generation by Text Mining and Gene Prioritization
Volume: 21 Issue: 8
Author(s): Ingrid Petric, Balazs Ligeti, Balazs Gyorffy and Sandor Pongor
Affiliation:
Keywords: Biomedical hypothesis generation, disease gene prediction, gene prioritization, ovarian cancer, text mining.
Abstract: Text mining methods can facilitate the generation of biomedical hypotheses by suggesting novel associations between diseases and genes. Previously, we developed a rare-term model called RaJoLink (Petric et al, J. Biomed. Inform. 42(2): 219-227, 2009) in which hypotheses are formulated on the basis of terms rarely associated with a target domain. Since many current medical hypotheses are formulated in terms of molecular entities and molecular mechanisms, here we extend the methodology to proteins and genes, using a standardized vocabulary as well as a gene/protein network model. The proposed enhanced RaJoLink rare-term model combines text mining and gene prioritization approaches. Its utility is illustrated by finding known as well as potential gene-disease associations in ovarian cancer using MEDLINE abstracts and the STRING database.
Export Options
About this article
Cite this article as:
Petric Ingrid, Ligeti Balazs, Gyorffy Balazs and Pongor Sandor, Biomedical Hypothesis Generation by Text Mining and Gene Prioritization, Protein & Peptide Letters 2014; 21 (8) . https://dx.doi.org/10.2174/09298665113209990063
DOI https://dx.doi.org/10.2174/09298665113209990063 |
Print ISSN 0929-8665 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5305 |
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
Related Articles
-
Oxaliplatin-mediated Inhibition of Survivin Increases Sensitivity of Head and Neck Squamous Cell Carcinoma Cell Lines to Paclitaxel
Current Cancer Drug Targets PI3K Inhibitors for Cancer Therapy: What has been Achieved So Far?
Current Medicinal Chemistry Antineoplastic Action of Growth Hormone-Releasing Hormone (GHRH) Antagonists
Recent Patents on Anti-Cancer Drug Discovery Hydroxysteroid Dehydrogenase (17β -HSD3, 17β-HSD5, and 3α-HSD3) Inhibitors:Extragonadal Regulation of Intracellular Sex Steroid Hormone Levels
Recent Patents on Endocrine, Metabolic & Immune Drug Discovery Natural Products Based Anticancer Agents
Mini-Reviews in Organic Chemistry T Cell Redirecting Therapies for Cancer Treatment
Current Cancer Drug Targets Advances in the Development of Class I Phosphoinositide 3-Kinase (PI3K) Inhibitors
Current Topics in Medicinal Chemistry Sentinel Lymph Node Mapping in Early Stage Endometrial Cancer Patients in Low-Resource Settings
Current Women`s Health Reviews NFκB Pathway and microRNA-9 and -21 are Involved in Sensitivity to the Pterocarpanquinone LQB-118 in Different CML Cell Lines
Anti-Cancer Agents in Medicinal Chemistry Cyclin Dependent Kinase 1 Inhibitors: A Review of Recent Progress
Current Medicinal Chemistry Targeted Enzyme Prodrug Therapies
Mini-Reviews in Medicinal Chemistry MicroRNAs as Regulators in Normal Hematopoietic and Leukemia Stem Cells: Current Concepts and Clinical Implications
Current Molecular Medicine Radionuclide Therapy of Cancer with Radiolabeled Antibodies
Anti-Cancer Agents in Medicinal Chemistry Deep Penetration of Nanoparticulate Drug Delivery Systems into Tumors: Challenges and Solutions
Current Medicinal Chemistry Spinophilin: A New Tumor Suppressor at 17q21
Current Molecular Medicine Mitogen-activated Protein Kinase Kinase 6-fusion Protein (MAP2K6-FP) Potentiates the Anti-tumor effects of Paclitaxel in Ovarian Cancer
Anti-Cancer Agents in Medicinal Chemistry ERK Signaling Pathway Regulates Embryonic Survival and Eye Development in Goldfish, Carassius auratus
Current Molecular Medicine Paris Saponin VII Induces Apoptosis and Cell Cycle Arrest in Erythroleukemia Cells by a Mitochondrial Membrane Signaling Pathway
Anti-Cancer Agents in Medicinal Chemistry MicroRNA-31 Inhibits Lung Adenocarcinoma Stem-Like Cells via Down-Regulation of MET-PI3K-Akt Signaling Pathway
Anti-Cancer Agents in Medicinal Chemistry A Role for Tumor Suppressor Protein p53 in the Fidelity of DNA Synthesis and Resistance Towards Nucleoside Analogs
Current Cancer Therapy Reviews