F-SNP: computationally predicted functional SNPs for disease association studies.
paper
Cited
Public
- Authors
- Lee, Phil Hyoun; Shatkay, Hagit
- Year
- 2008
- Journal
- Nucleic acids research
- PMID
- 17986460
- DOI
- 10.1093/nar/gkm904
- PMCID
- PMC2238878
The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from 16 bioinformatics tools and databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. As such, the database helps identify and focus on SNPs with potential deleterious effect to human health. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. A web interface enables easy navigation for obtaining information through multiple starting points and exploration routes (e.g. starting from SNP identifier, genomic region, gene or target disease). The F-SNP database is available at http://compbio.cs.queensu.ca/F-SNP/.
Decision procedure for functional SNP assessment. Each SNP is examined for deleterious effects with respect to each functional category (i.e. protein coding, splicing regulation, transcriptional regulation and post-translationβas shown in the top part of the figure). For each category, a series of tests is executed to determine whether the SNP has a functional impact. First the type (coding, intronic, etc.) of the genomic region is identified, using data from dbSNP (3) and Ensembl (4). Once this is determined, other tests are performed. For example, to assess if a SNP has a deleterious effect on protein coding, it first must be located on a coding region. Ensembl (4) is used to examine if this is a nonsense mutation, in which case the SNP is considered to be deleterious. Otherwiseβif the SNP is a missense mutation, it is further tested by five different tools [PolyPhen (6), SIFT (7), SNPeffect (8), SNPs3D (9) and LS-SNP (10)] to check if the non-synonymous substitution is deleterious. A majority vote among these tools concludes the process, and identifies the SNP as either having a potentially deleterious functional impact (denoted βfunctionalβ in the figure) or not.
Example of an F-SNP search session. (a) The initial search page is displayed, where the user selected the disease type to be Cancers, and the specific disease to be Breast cancer (Search by disease). (b) Results obtained after clicking the Submit button in panel (a), namely a list of genes associated with Breast cancer along with their associated chromosome location, known related disorders, and links to OMIM. The BRCA1 link (circled) is selected and clicked. (c) A detailed description of SNPs associated with BRCA1 is produced (demonstrating results of Search by gene). The SNP whose identifier is rs28897699 (circled)βindicated by a β+β mark to have associated functional informationβis selected and clicked. (d) Information about the SNP rs28897699 is presented (demonstrating results of Search by SNP ID).
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| 20 | Figure 2. | Example of an F-SNP search session. (a) The initial search page is displayed, where the user⦠|
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| A polymorphism in the histone deacetylase 1 gene is associated with the response to corticosteroids in asthmatics. | Kim MH et al. | β | 2013 | β |
| A replication study from Chinese supports association between lupus-risk allele in TNFSF4 and renal disorder. | Zhou XJ et al. | β | 2013 | β |
| Association of a common genetic variant of the IGF-1 gene with event-free survival in patients with HER2-positive breast cancer. | Muendlein A et al. | β | 2013 | β |
| Association of CDKN1B gene polymorphisms with susceptibility to breast cancer: a meta-analysis. | Xiang H et al. | β | 2013 | β |
| Association of genes of protease-antiprotease balance pathway to lung function and emphysema subtypes. | Kukkonen MK et al. | β | 2013 | β |
| Association of liver X receptors (LXRs) genetic variants to gallbladder cancer susceptibility. | Sharma KL et al. | β | 2013 | β |
| Association of potentially functional genetic variants of PLCE1 with gallbladder cancer susceptibility in north Indian population. | Sharma KL et al. | β | 2013 | β |
| Association of XRCC3 and XRCC4 gene polymorphisms, family history of cancer and tobacco smoking with non-small-cell lung cancer in a Chinese population: a case-control study. | He F et al. | β | 2013 | β |
| Associations of oxidative balance-related exposures with incident, sporadic colorectal adenoma according to antioxidant enzyme genotypes. | Labadie J et al. | β | 2013 | β |
| Bim polymorphisms: influence on function and response to treatment in children with acute lymphoblastic leukemia. | GagnΓ© V et al. | β | 2013 | β |
| Breast cancer prediction using genome wide single nucleotide polymorphism data. | Hajiloo M et al. | β | 2013 | β |
| CD44 gene polymorphisms in breast cancer risk and prognosis: a study in North Indian population. | Tulsyan S et al. | β | 2013 | β |
| Common gene variants in RAD51, XRCC2 and XPD are not associated with clinical outcome in soft-tissue sarcoma patients. | Szkandera J et al. | β | 2013 | β |
| Comprehensive SNP scan of DNA repair and DNA damage response genes reveal multiple susceptibility loci conferring risk to tobacco associated leukoplakia and oral cancer. | Mondal P et al. | β | 2013 | β |
| Conditional testing of multiple variants associated with bone mineral density in the FLNB gene region suggests that they represent a single association signal. | Mullin BH et al. | β | 2013 | β |
| Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools. | Castellana S et al. | β | 2013 | β |
| DCC (deleted in colorectal carcinoma) gene variants confer increased susceptibility to gallbladder cancer (Ref. No.: Gene-D-12-01446). | Rai R et al. | β | 2013 | β |
| Discovery by the Epistasis Project of an epistatic interaction between the GSTM3 gene and the HHEX/IDE/KIF11 locus in the risk of Alzheimer's disease. | Bullock JM et al. | β | 2013 | β |
| DNA marker applications to molecular genetics and genomics in tomato. | Shirasawa K et al. | β | 2013 | β |
| Genetic dissection of the pre-eclampsia susceptibility locus on chromosome 2q22 reveals shared novel risk factors for cardiovascular disease. | Johnson MP et al. | β | 2013 | β |
| Genetic variations in TERT-CLPTM1L locus are associated with risk of lung cancer in Chinese population. | Zhong R et al. | β | 2013 | β |
| Genome-wide SNP genotyping to infer the effects on gene functions in tomato. | Hirakawa H et al. | β | 2013 | β |
| Identifying SNP targeted pathways in partial epilepsies with genome-wide association study data. | Bakir-Gungor B et al. | β | 2013 | β |
| Intron 3 of the ARID5B gene: a hot spot for acute lymphoblastic leukemia susceptibility. | GutiΓ©rrez-Camino Γ et al. | β | 2013 | β |
| Lack of correlation between in silico projection of function and quantitative real-time PCR-determined gene expression levels in colon tissue. | Penney RB et al. | β | 2013 | β |
| Leucine to proline substitution by SNP at position 197 in Caspase-9 gene expression leads to neuroblastoma: a bioinformatics analysis. | Kundu A et al. | β | 2013 | β |
| Molecular markers to predict outcome to antiangiogenic therapies in colorectal cancer: current evidence and future perspectives. | Custodio A et al. | β | 2013 | β |
| Myosin Vb gene is associated with schizophrenia in Chinese Han population. | Chen Y et al. | β | 2013 | β |
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| Pharmacogenetic angiogenesis profiling for first-line chemotherapy in patients with advanced gastric cancer. | Dan S et al. | β | 2013 | β |
| Polymorphisms in the gene regions of the adaptor complex LAMTOR2/LAMTOR3 and their association with breast cancer risk. | De Araujo ME et al. | β | 2013 | β |
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| Prognostic role of lemur tyrosine kinase-3 germline polymorphisms in adjuvant gastric cancer in Japan and the United States. | Wakatsuki T et al. | β | 2013 | β |
| RGS5 gene and therapeutic response to short acting bronchodilators in paediatric asthma patients. | Labuda M et al. | β | 2013 | β |
| rs189037, a functional variant in ATM gene promoter, is associated with idiopathic nonobstructive azoospermia. | Li Z et al. | β | 2013 | β |
| SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. | Merelli I et al. | β | 2013 | β |
| The identification of pathway markers in intracranial aneurysm using genome-wide association data from two different populations. | Bakir-Gungor B et al. | β | 2013 | β |
| TNFRSF10B polymorphisms and haplotypes associated with increased risk of death in non-small cell lung cancer. | Schabath MB et al. | β | 2013 | β |
| Towards precision medicine: advances in computational approaches for the analysis of human variants. | Peterson TA et al. | β | 2013 | β |
| Towards understanding the low prevalence of Helicobacter pylori in Malays: genetic variants among Helicobacter pylori-negative ethnic Malays in the north-eastern region of Peninsular Malaysia and Han Chinese and South Indians. | Maran S et al. | β | 2013 | β |
| A genome-wide association study identifies KNG1 as a genetic determinant of plasma factor XI Level and activated partial thromboplastin time. | Sabater-Lleal M et al. | β | 2012 | β |
| Analysis of functional germline polymorphisms for prediction of response to anthracycline-based neoadjuvant chemotherapy in breast cancer. | Szkandera J et al. | β | 2012 | β |
| An association between polymorphism of the heme oxygenase-1 and -2 genes and age-related macular degeneration. | Synowiec E et al. | β | 2012 | β |
| Association between polymorphisms of the DNA base excision repair genes MUTYH and hOGG1 and age-related macular degeneration. | Synowiec E et al. | β | 2012 | β |
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| Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing. | Liu Q et al. | β | 2012 | β |
| Gender differences in associations of glutamate decarboxylase 1 gene (GAD1) variants with panic disorder. | Weber H et al. | β | 2012 | β |
| Genetic polymorphisms and protein expression of NRF2 and Sulfiredoxin predict survival outcomes in breast cancer. | Hartikainen JM et al. | β | 2012 | β |
| GWASdb: a database for human genetic variants identified by genome-wide association studies. | Li MJ et al. | β | 2012 | β |
| Insulin-like growth factor axis gene polymorphisms modify risk of pancreatic cancer. | Dong X et al. | β | 2012 | β |
| Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. | Izarzugaza JM et al. | β | 2012 | β |
| Mechanisms of loss of functions of human angiogenin variants implicated in amyotrophic lateral sclerosis. | Padhi AK et al. | β | 2012 | β |
| Post-GWAS functional characterization of susceptibility variants for chronic lymphocytic leukemia. | SillΓ© FC et al. | β | 2012 | β |
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| Role of rare variants in undetermined multiple adenomatous polyposis and early-onset colorectal cancer. | Lefevre JH et al. | β | 2012 | β |
| Role of SNAP25 explored in eastern Indian attention deficit hyperactivity disorder probands. | Sarkar K et al. | β | 2012 | β |
| Rs1076560, a functional variant of the dopamine D2 receptor gene, confers risk of schizophrenia in Han Chinese. | Zheng C et al. | β | 2012 | β |
| Significant role of estrogen and progesterone receptor sequence variants in gallbladder cancer predisposition: a multi-analytical strategy. | Srivastava A et al. | β | 2012 | β |
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| Association between somatostatin receptor 5 gene polymorphisms and pancreatic cancer risk and survival. | Li D et al. | β | 2011 | β |
| Common cancer stem cell gene variants predict colon cancer recurrence. | Gerger A et al. | β | 2011 | β |
| Contribution of a common variant in the promoter of the 1-Ξ±-hydroxylase gene (CYP27B1) to fracture risk in the elderly. | Clifton-Bligh RJ et al. | β | 2011 | β |
| Data integration workflow for search of disease driving genes and genetic variants. | Karinen S et al. | β | 2011 | β |
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| DNA mismatch repair gene polymorphisms affect survival in pancreatic cancer. | Dong X et al. | β | 2011 | β |
| Evaluation of functional genetic variants for breast cancer risk: results from the Shanghai breast cancer study. | Zhang B et al. | β | 2011 | β |
| Genomewide linkage analysis in Costa Rican families implicates chromosome 15q14 as a candidate region for OCD. | Ross J et al. | β | 2011 | β |
| Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites. | Faber K et al. | β | 2011 | β |
| Glucose metabolism gene polymorphisms and clinical outcome in pancreatic cancer. | Dong X et al. | β | 2011 | β |
| Glucose metabolism gene variants modulate the risk of pancreatic cancer. | Dong X et al. | β | 2011 | β |
| ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework. | Zhang K et al. | β | 2011 | β |
| Meet me halfway: when genomics meets structural bioinformatics. | Gong S et al. | β | 2011 | β |
| pfSNP: An integrated potentially functional SNP resource that facilitates hypotheses generation through knowledge syntheses. | Wang J et al. | β | 2011 | β |
| Pharmacogenetic angiogenesis profiling for first-line Bevacizumab plus oxaliplatin-based chemotherapy in patients with metastatic colorectal cancer. | Gerger A et al. | β | 2011 | β |
| Phosphodiesterase type 4D gene polymorphism: association with the response to short-acting bronchodilators in paediatric asthma patients. | Labuda M et al. | β | 2011 | β |
| Single-nucleotide polymorphisms at five loci are associated with C-reactive protein levels in a cohort of Filipino young adults. | Curocichin G et al. | β | 2011 | β |
| Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk. | Reynolds CA et al. | β | 2010 | β |
| An improved in silico selection of phenotype affecting polymorphisms in SLC6A4, HTR1A and HTR2A genes. | Piva F et al. | β | 2010 | β |
| ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. | Wang K et al. | β | 2010 | β |
| Association analysis of susceptibility candidate region on chromosome 5q31 for tuberculosis. | Ridruechai C et al. | β | 2010 | β |
| FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. | Goodswen SJ et al. | β | 2010 | β |
| Genetic variation in genes interacting with BRCA1/2 and risk of breast cancer in the Cypriot population. | Loizidou MA et al. | β | 2010 | β |
| Insulin-like growth factor axis gene polymorphisms and clinical outcomes in pancreatic cancer. | Dong X et al. | β | 2010 | β |
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| Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. | Hijikata A et al. | β | 2010 | β |
| New mutations in APOB100 involved in familial hypobetalipoproteinemia. | Brusgaard K et al. | β | 2010 | β |
| Polymorphisms of the UCP2 gene are associated with proliferative diabetic retinopathy in patients with diabetes mellitus. | Crispim D et al. | β | 2010 | β |
| Selection and mutation in the "new" genetics: an emerging hypothesis. | Gottlieb B et al. | β | 2010 | β |
| SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. | Saccone SF et al. | β | 2010 | β |
| Association of DLC1 gene polymorphism with susceptibility to hepatocellular carcinoma in Chinese hepatitis B virus carriers. | Dong X et al. | β | 2009 | β |
| A survey of ABCA1 sequence variation confirms association with dementia. | Reynolds CA et al. | β | 2009 | β |
| Genomics software: The view from 10,000 feet. | Weale ME | β | 2009 | β |
| Next generation tools for the annotation of human SNPs. | Karchin R | β | 2009 | β |
| Predicting potentially functional SNPs in drug-response genes. | Pang GS et al. | β | 2009 | β |
| Pro12Ala polymorphism of the peroxisome proliferatoractivated receptor-gamma gene is associated with metabolic syndrome and surrogate measures of insulin resistance in healthy men: interaction with smoking status. | Tellechea ML et al. | β | 2009 | β |
| Single-nucleotide polymorphic variants of human glutathione transferase T1-1 differ in stability and functional properties. | Josephy PD et al. | β | 2009 | β |
| Systematic evaluation of the effect of common SNPs on pre-mRNA splicing. | ElSharawy A et al. | β | 2009 | β |
| The variant rs1867277 in FOXE1 gene confers thyroid cancer susceptibility through the recruitment of USF1/USF2 transcription factors. | Landa I et al. | β | 2009 | β |
| Functional analysis of novel SNPs and mutations in human and mouse genomes. | Liu CK et al. | β | 2008 | β |
| Functional genomics and SNP analysis of human genes encoding proline metabolic enzymes. | Hu CA et al. | β | 2008 | β |
| Ranking single nucleotide polymorphisms by potential deleterious effects. | Lee PH et al. | β | 2008 | β |
| Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. | Saccone SF et al. | β | 2008 | β |