Text mining and network analysis to find functional associations of genes in high altitude diseases
Computational Biology and ChemistryPublished 2 May 2018
Balu Bhasuran, Devika Subramanian, Jeyakumar Natarajan
Citations14
SJR quartileQ2
SJR score0.52
SNIP0.71
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
The network constructed from this study proposes a large number of genes that work in-toto in high altitude conditions, and provides a good reference for further study of the genetic relationships inHigh altitude diseases.
Abstract
The network constructed from this study proposes a large number of genes that work in-toto in high altitude conditions. Overall, the result provides a good reference for further study of the genetic relationships in high altitude diseases.
Keywords
Biochemistry, Genetics and Molecular Biology
Genome ResearchCytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
54,321 Citations2003Paul Shannon, Andrew Markiel +7 more
Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
BMC BioinformaticsAn automated method for finding molecular complexes in large protein interaction networks
6,293 Citations2003Gary D. Bader, Christopher W.V. Hogue
A novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes is described.
Nucleic Acids ResearchSTRING v9.1: protein-protein interaction networks, with increased coverage and integration
4,492 Citations2012Andrea Franceschini, Damian Szklarczyk +9 more
The update to version 9.1 of STRING is described, introducing several improvements, including extending the automated mining of scientific texts for interaction information, to now also include full-text articles, and providing users with statistical information on any functional enrichment observed in their networks.
Nucleic Acids ResearchOnline Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
3,512 Citations2004Ada Hamosh
Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support human genetics research and education and the practice of clinical genetics.
Machine LearningText Classification from Labeled and Unlabeled Documents using EM
2,749 Citations2000Kamal Nigam, Andrew Kachites McCallum +2 more
This paper shows that the accuracy of learned text classifiers can be improved by augmenting a small number of labeled training documents with a large pool of unlabeled documents, and presents two extensions to the algorithm that improve classification accuracy under these conditions.
Nucleic Acids ResearchEntrez Gene: gene-centered information at NCBI
2,152 Citations2010Donna Maglott, James Ostell +2 more
The content in Entrez Gene represents the integration of curation and automated processing from NCBI’s Reference Sequence project (RefSeq), collaborating model organism databases, consortia such as Gene Ontology and other databases within NCBI.
The EMBO JournalHIF prolyl‐hydroxylase 2 is the key oxygen sensor setting low steady‐state levels of HIF‐1α in normoxia
1,342 Citations2003Edurne Berra, Emmanuel Benizri +4 more
It is shown that specific ‘silencing’ of PHD2 with short interfering RNAs is sufficient to stabilize and activate HIF‐1α in normoxia in all the human cells investigated, concluding that, in vivo, PHDs have distinct assigned functions.
DatabaseDisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes
1,177 Citations2015Janet Piñero, Núria Queralt-Rosiñach +6 more
One of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic origin, designed to fulfill the needs of different user profiles, are offered.
Untangling text data mining
856 Citations1999Marti A. Hearst
Data mining, information access, and corpus-based computational linguistics are defined and the relationship of these to text data mining is discussed, and the intent behind these contrasts is to draw attention to exciting new kinds of problems for computational linguists.
Briefings in BioinformaticsA survey of current work in biomedical text mining
767 Citations2005Aaron Cohen
The major challenge of biomedical text mining over the next 5-10 years will require enhanced access to full text, better understanding of the feature space of biomedical literature, better methods for measuring the usefulness of systems to users, and continued cooperation with the biomedical research community to ensure that their needs are addressed.
Nature GeneticsA literature network of human genes for high-throughput analysis of gene expression.
760 Citations2001Tor‐Kristian Jenssen, Astrid Lægreid +2 more
Nature Reviews GeneticsLiterature mining for the biologist: from information retrieval to biological discovery
635 Citations2006Lars Juhl Jensen, Jasmin Šarić +1 more
This work states that literature mining is also becoming useful for both hypothesis generation and biological discovery, however, the latter will require the integration of literature and high-throughput data, which should encourage close collaborations between biologists and computational linguists.
BioinformaticsRelEx—Relation extraction using dependency parse trees
569 Citations2006Katrin Fundel, Robert Küffner +1 more
BANNER: AN EXECUTABLE SURVEY OF ADVANCES IN BIOMEDICAL NAMED ENTITY RECOGNITION
487 Citations2007Robert Leaman, Graciela Gonzalez‐Hernandez
BANNER is an open-source, executable survey of advances in biomedical named entity recognition, intended to serve as a benchmark for the field and is designed to maximize domain independence by not employing brittle semantic features or rule-based processing steps.
Nature GeneticsA literature network of human genes for high-throughput analysis of gene expression
484 Citations2001Tor-Kristian Jenssen, Astrid Lægreid +2 more
Briefings in BioinformaticsGraph-based methods for analysing networks in cell biology
435 Citations2006Tero Aittokallio
Molecular Biology and EvolutionGenetic Variations in Tibetan Populations and High-Altitude Adaptation at the Himalayas
403 Citations2010Yi Peng, Zhaohui Yang +13 more
Analysis of genome-wide sequence variations in Tibetans indicates strong signals of selective sweep in two hypoxia-related genes, EPAS1 and EGLN1, and suggests that during the long-term occupation of high-altitude areas, the functional sequence variations for acquiring biological adaptation to high-Altitude Hypoxia have been enriched in Tibetan populations.
Genes & DevelopmentHuman high-altitude adaptation: forward genetics meets the HIF pathway
351 Citations2014Abigail W. Bigham, Frank S. Lee
A review of recent genome-wide studies on human adaptation to high altitude finds genetic signatures have been identified in the hypoxia-inducible factor (HIF) pathway, which orchestrates the transcriptional response tohypoxia.
Molecular Biology and EvolutionA Genome-Wide Search for Signals of High-Altitude Adaptation in Tibetans
342 Citations2010Shuhua Xu, S. Li +11 more
Trends in biotechnologyText mining and its potential applications in systems biology
332 Citations2006Sophia Ananiadou, Douglas B. Kell +1 more
By adding meaning to text, text mining techniques produce a more structured analysis of textual knowledge than simple word searches, and can provide powerful tools for the production and analysis of systems biology models.
Genome biologyOverview of BioCreative II gene normalization
329 Citations2008Alexander A. Morgan, Zhiyong Lu +18 more
Major advances for the BioCreative II gene normalization task include broader participation (20 versus 8 teams) and a pooled system performance comparable to human experts, at over 90% agreement, which show promise as tools to link the literature with biological databases.
American Journal of Respiratory and Critical Care MedicineHigh-Altitude Medicine
294 Citations2012John B. West
The two major human populations that have adapted well to high altitude, the Tibetans and Andeans, have strikingly different phenotypes and important recent advances have been made on mitigation of the effects of the hypoxic environment.
Journal of the American Society for Information Science and TechnologyText mining: Generating hypotheses from MEDLINE
284 Citations2003Padmini Srinivasan
This report presents open and closed text mining algorithms that are built within the discovery framework established by Swanson and Smalheiser and successfully generate ranked term lists where the key terms representing novel relationships between topics are ranked high.
BIOBIBLIOMETRICS: INFORMATION RETRIEVAL AND VISUALIZATION FROM CO-OCCURRENCES OF GENE NAMES IN MEDLINE ABSTRACTS
272 Citations1999Benjamin J. Stapley, G. Benoît
A prototype system for retrieving and visualizing information from literature and genomic databases using gene names, which is a tool for efficiently exploring the biomedical information landscape and may act as a inference network.
The American Journal of Human GeneticsLinkage and Association Analysis of Angiotensin I–Converting Enzyme (ACE)–Gene Polymorphisms with ACE Concentration and Blood Pressure
269 Citations2001Xiaofeng Zhu, Nourdine Bouzekri +8 more
It is found that the two polymorphisms explaining the greatest variation in ACE concentration are significantly associated with BP, through interaction, in this African population sample, demonstrating that allelic interaction may play an important role in the dissection of complex traits such as BP.
Nucleic Acids ResearchPolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites
256 Citations2008Dongping Cheng, Craig Knox +4 more
The PolySearch web server, a web-based tool that supports comprehensive queries in genomics, proteomics or metabolomics, and exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences.
BioTechniquesMedMiner: An Internet Text-Mining Tool for Biomedical Information, with Application to Gene Expression Profiling
253 Citations1999Lorraine Tanabe, Uwe Scherf +4 more
An Internet-based hypertext program, MedMiner, which filters and organizes large amounts of textual and structured information returned from public search engines like GeneCards and PubMed, and can be used to organize the information returning from any arbitrary PubMed search.
MINING MEDLINE: ABSTRACTS, SENTENCES, OR PHRASES?
244 Citations2001Jie Ding, Daniel Berleant +2 more
Comparing abstracts, sentences, and phrases in MEDLINE using the standard information retrieval performance measures of recall, precision, and effectiveness, for the task of mining interactions among biochemical terms based on term co-occurrence shows statistically significant differences that can impact the choice of text unit.
Emergency Medicine Clinics of North AmericaHigh-altitude illness
215 Citations2004Scott A. Gallagher, Peter H. Hackett
Practical practitioners working in or advising those traveling to a high altitude must be familiar with the early recognition of symptoms, prompt and appropriate therapy, and proper preventative measures for high-altitude illness.
BioinformaticsKnowledge discovery by automated identification and ranking of implicit relationships
213 Citations2004Jonathan D. Wren, Raffi Bekeredjian +3 more
A computational method to identify relationships within scientific reports, such that large sets of relationships between unrelated items could be sought out and statistically ranked for their potential relevance as a set, demonstrates the method is well suited to discover novel relationships based upon existing shared relationships.
BMC BioinformaticsPubMatrix: a tool for multiplex literature mining
209 Citations2003Kevin G. Becker, Douglas A Hosack +5 more
PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence, which can be assigned genetic, biological, or clinical relevance in a rapid flexible systematic fashion.
High Altitude Medicine & BiologyAltitude Adaptation: A Glimpse Through Various Lenses
157 Citations2015Tatum S. Simonson
Genomic findings parallel observations conveyed by decades of physiological research: different continental populations, resident at high altitude for hundreds of generations, exhibit a distinct composite of traits at altitude, which will advance the understanding of both adaptive and non-adaptive responses to hypoxia.
Nucleic Acids ResearchPolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more
148 Citations2015Yifeng Liu, Yongjie Liang +1 more
PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records to facilitate user interpretation.
CellEGLN1 Inhibition and Rerouting of α-Ketoglutarate Suffice for Remote Ischemic Protection
143 Citations2016Benjamin A. Olenchock, Javid J. Moslehi +14 more
It is found that inhibiting Egln1 systemically or in skeletal muscles protects mice against myocardial ischemia-reperfusion (I/R) injury and RIPC in this latter model was mediated by a secreted factor.
Journal of Applied PhysiologyBarometric pressures at extreme altitudes on Mt. Everest: physiological significance
137 Citations1983John B. West, S. Lahiri +3 more
Although the mountain has been climbed without supplementary O2, the very low O2 partial pressure at the summit means that it is at the limit of man's tolerance, and even day-by-day variations in barometric pressure apparently affect maximal O2 uptake.
Genome biologyMining microarray expression data by literature profiling
136 Citations2002Damien Chaussabel, Alan Sher
A mining technique based on the analysis of literature profiles generated by extracting the frequencies of certain terms from thousands of abstracts stored in the Medline literature database is developed, which constitutes a means of exploring the biological significance of large and heterogeneous lists of genes.
Data and Information Visualization Methods, and Interactive Mechanisms: A Survey
126 Citations2011Khan Muzammil, Shah Khan Sarwar
The purpose of this piece of document is to collect all visualization techniques with their brief introduction to form a guide for the young researchers who wants to start work in visualization.
International Journal of Medical InformaticsGetting to the (c)ore of knowledge: mining biomedical literature
124 Citations2002Berry de Bruijn, Joel Martin
The present article describes the range of text mining techniques that have been applied to scientific documents and divides 'automated reading' into four general subtasks: text categorization, named entity tagging, fact extraction, and collection-wide analysis.
Integrative and Comparative BiologyHuman responses to extreme altitudes
121 Citations2006John B. West
The most important physiological response to extreme altitude is extreme hyperventilation which, on the summit of Mt. Everest, drives the alveolar P(CO(2)) down to 7-8 mmHg and increases the oxygen affinity of hemoglobin, a response which the successful climber shares with many other animals in oxygen-deprived environments.
Emergency Medicine Clinics of North AmericaHIGH-ALTITUDE MEDICINE
109 Citations1997Ken Zafren, Benjamin Honigman
The issue of patients with underlying diseases who wish to travel to high-altitude destinations and Physicians advising travelers and trekkers who will be visiting high-ALTitude areas will find an organized approach to giving pretravel advice.
BioinformaticsExtracting synonymous gene and protein terms from biological literature
103 Citations2003Hong Yu, Eugene Agichtein
Four complementary approaches for extracting gene and protein synonyms from text are explored, namely the unsupervised, partially supervised, and supervised machine-learning techniques, as well as the manual knowledge-based approach.
Journal of the American Society for Information Science and TechnologyConstructing an associative concept space for literature‐based discovery
71 Citations2004C. Christiaan van der Eijk, Erik M. van Mulligen +3 more
PLoS ONEText Mining the History of Medicine
62 Citations2016Paul M. Thompson, Riza Batista-Navarro +7 more
Evidence from diverse historical medical documents from different periods is used to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed.
Proceedings of the 37th annual meeting of the Association for Computational Linguistics on Computational Linguistics -
48 Citations1999
This volume contains the papers accepted for presentation at the 37th Annual Meeting of the Association for Computational Linguistics, held at the University of Maryland from 20th to 26th June 1999.
High Altitude Medicine & BiologyGenetic Variation in <i>SENP1</i> and <i>ANP32D</i> as Predictors of Chronic Mountain Sickness
32 Citations2014Amy M. Cole, Nayia Petousi +2 more
Results provide independent evidence in support of a role for SENP1 in CMS in individuals of Quechua ancestry and suggest the SENP1 and ANP32D signatures of selection are in tight linkage disequilibrium (LD).
International Journal of BiometeorologyAssociation of high-altitude systemic hypertension with the deletion allele-of the angiotensin-converting enzyme (ACE) gene
31 Citations2003Ratan Kumar, M. A. Qadar Pasha +7 more
It is suggested that environmental changes and pre-existing genetic factors, namely the ACE D allele, might be two of the factors predisposing natives of low altitudes to systemic hypertension, a polygenic disease, at high altitude.
Experimental HematologySENP1, but not fetal hemoglobin, differentiates Andean highlanders with chronic mountain sickness from healthy individuals among Andean highlanders
22 Citations2016Matthew M. Hsieh, David Callacondo +9 more
HbF levels were normal and other classic erythropoietic parameters did not differ between healthy and CMS individuals, however, the non-G/G genotypes of SENP1 appeared to differentiate individuals with CMS from healthy Andean highlanders.
AndrologiaHigher androgen bioactivity is associated with excessive erythrocytosis and chronic mountain sickness in Andean Highlanders: a review
22 Citations2014Gustavo F. Gonzáles, D. Chaupis
Findings on role of serum T levels on adaptation at HA and genes acting on this process are summarised and increased androgen activity is related with CMS.
International Journal of Data Mining and BioinformaticsA hybrid named entity tagger for tagging human proteins/genes
19 Citations2014Kalpana Raja, Suresh Subramani +1 more
A new hybrid approach based on a machine learning algorithm (conditional random fields), set of (manually constructed) rules, and a novel abbreviation identification algorithm to surmount the common errors observed in available taggers to tag human genes/proteins is proposed.
