An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junle; Khoury, Muin J.; Gwinn, Marta

doi:10.1186/1471-2105-8-436

Cited by 14 publications

(11 citation statements)

References 14 publications

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“…HuGE Navigator database is an integrated, searchable, Web-based knowledge base which mines the scientific literature on human genetic associations and human genome epidemiology [29, 30]. In HuGE Navigator, common genes (score > 5) in PI, CF and Liver Disease were CFTR, SPINK1, GSTP1, PRSS1, ADRB2, GSTM1, GSTT1, HRAS, MIF, OGG1 and TNF.…”

Section: Resultsmentioning

confidence: 99%

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In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis

2017

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Cystic Fibrosis is the most common lethal autosomal recessive disorder in the white population, affecting among other organs, the lung, the pancreas and the liver. Whereas Cystic Fibrosis is a monogenic disease, many studies reveal a very complex relationship between genotype and clinical phenotype. Indeed, the broad phenotypic spectrum observed in Cystic Fibrosis is far from being explained by obvious genotype-phenotype correlations and it is admitted that Cystic Fibrosis disease is the result of multiple factors, including effects of the environment as well as modifier genes. Our objective was to highlight new modifier genes with potential implications in the lung, pancreatic and liver outcomes of the disease. For this purpose we performed a system biology approach which combined, database mining, literature mining, gene expression study and network analysis as well as pathway enrichment analysis and protein-protein interactions. We found that IFI16, CCNE2 and IGFBP2 are potential modifiers in the altered lung function in Cystic Fibrosis. We also found that EPHX1, HLA-DQA1, HLA-DQB1, DSP and SLC33A1, GPNMB, NCF2, RASGRP1, LGALS3 and PTPN13, are potential modifiers in pancreas and liver, respectively. Associated pathways indicate that immune system is likely involved and that Ubiquitin C is probably a central node, linking Cystic Fibrosis to liver and pancreatic disease. We highlight here new modifier genes with potential implications in Cystic Fibrosis. Nevertheless, our in silico analysis requires functional analysis to give our results a physiological relevance.

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Section: Resultsmentioning

confidence: 99%

“…In HuGE Navigator we used the CF, PI and Liver Disease key words. The genes with a genetic association above 5 were selected (score formula is described in [30]).…”

Section: Methodsmentioning

confidence: 99%

In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis

2017

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“…In addition, genes indexed in the HuGE literature database can be used to identify relevant candidate genes. The detailed schema for the HuGE Navigator database can be found in the paper by Yu et al 4 …”

Section: Methodsmentioning

confidence: 99%

GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies

Yesupriya

Wulf

et al. 2011

Eur J Hum Genet

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“…Gene Prospector was developed as a component of HuGE Navigator, an integrated, searchable, Web-based knowledge base of genetic associations and human genome epidemiology. The HuGE Navigator knowledge base was developed on an open-source infrastructure developed by Yu, et al[ 8 ]. The Gene Prospector was built by using J2EE technology [ 9 ] and on other Java open-source frameworks such as Hibernate [ 10 ] and Strut [ 11 ].…”

Section: Methodsmentioning

confidence: 99%

“…Entrez Gene records from NCBI Entrez Gene database [ 15 ] are used as standards for gene information. The detailed schema for the literature database can be found in reference [ 8 ].…”

Section: Methodsmentioning

confidence: 99%

Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases

Wulf

Liu

et al. 2008

BMC Bioinformatics

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Background: Millions of single nucleotide polymorphisms have been identified as a result of the human genome project and the rapid advance of high throughput genotyping technology. Genetic association studies, such as recent genome-wide association studies (GWAS), have provided a springboard for exploring the contribution of inherited genetic variation and gene/environment interactions in relation to disease. Given the capacity of such studies to produce a plethora of information that may then be described in a number of publications, selecting possible disease susceptibility genes and identifying related modifiable risk factors is a major challenge. A Web-based application for finding evidence of such relationships is key to the development of follow-up studies and evidence for translational research.

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An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

Cited by 14 publications

References 14 publications

In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis

In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis

GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies

Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases

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