PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways.
paper
Cited
Public
- Authors
- Bhattacharya, Anindya; Ziebarth, Jesse D; Cui, Yan
- Year
- 2014
- Journal
- Nucleic acids research
- PMID
- 24163105
- DOI
- 10.1093/nar/gkt1028
- PMCID
- PMC3965097
Polymorphisms in microRNAs (miRNAs) and their target sites (PolymiRTS) are known to disrupt miRNA function, leading to the development of disease and variation in physiological and behavioral phenotypes. Here, we describe recent updates to the PolymiRTS database (http://compbio.uthsc.edu/miRSNP), an integrated platform for analyzing the functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sites. Recent advances in genomic technologies have made it possible to identify miRNA-mRNA binding sites from direct mapping experiments such as CLASH (cross linking, ligation and sequencing of hybrids). We have integrated data from CLASH experiments in the PolymiRTS database to provide more complete and accurate miRNA-mRNA interactions. Other significant new features include (i) small insertions and deletions in miRNA seed regions and miRNA target sites, (ii) TargetScan context + score differences for assessing the impact of polymorphic miRNA-mRNA interactions and (iii) biological pathways. The browse and search pages of PolymiRTS allow users to explore the relations between the PolymiRTSs and gene expression traits, physiological and behavioral phenotypes, human diseases and biological pathways.
Overview of the PolymiRTS database contents and screenshots of two new functions: browsing miRNA targets identified by CLASH experiments and illustrating genes with polymorphic miRNA target site in the contexts of biological pathways.
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| Name | Type |
|---|---|
| acute lymphocytic leukemia local | phenotype |
| AGO1 local | gene |
| AGTR1 local | gene |
| Alzheimerβs disease | phenotype |
| biological pathways | phenotype |
| blood pressure | phenotype |
| cancer | phenotype |
| cervical cancer local | phenotype |
| CLASH local | drug |
| complex traits | phenotype |
| conserved miRNA site local | phenotype |
| dbGaP | cohort |
| derived allele local | variant |
| diabetes | phenotype |
| disease | phenotype |
| eQTL data local | phenotype |
| experimentally supported miRNAβmRNA interactions local | drug |
| experimentally supported miRNA target sites with polymorphisms local | drug |
| GeneNetwork local | cohort |
| germ line mutation local | variant |
| GTEx eQTL browser local | cohort |
| GWAS data local | phenotype |
| has-miR-128b local | drug |
| has-miR-146a local | drug |
| hepatocellular carcinoma | phenotype |
| HT local | drug |
| HTL local | drug |
| human | cohort |
| human diseases local | phenotype |
| indel | variant |
| LT local | drug |
| LTL local | drug |
| mice | cohort |
| miR-122 local | drug |
| miR-122 binding site insertion local | variant |
| miR-155 local | drug |
| miR-200b-a-429 cluster local | drug |
| miR-200b-a-429 promoter polymorphism local | variant |
| miR-657 local | drug |
| miR-657 target site deletion local | variant |
| miRecords local | drug |
| miRISC local | drug |
| miRNA | drug |
| miRNA dysregulation local | phenotype |
| miRNA seed INDEL local | variant |
| miRNA seed SNP local | variant |
| miRNA targeting local | phenotype |
| miRNA target sites local | drug |
| miRTarBase local | drug |
| mouse QTL data local | phenotype |
| mRNA | drug |
| mutations | variant |
| N local | drug |
| new miRNA site local | phenotype |
| NHGRI-EBI GWAS catalog | cohort |
| nonconserved miRNA site local | phenotype |
| non-small cell lung cancer | phenotype |
| Parkinsonβs disease | phenotype |
| PolymiRTS database local | cohort |
| PolymiRTS database local | drug |
| Polymorphism | cohort |
| pre-miR-146a polymorphism local | variant |
| pri-miR-128b polymorphism local | variant |
| reference allele | variant |
| rs5186 local | variant |
| small INDELs local | variant |
| SNP | cohort |
| SomamiR database local | cohort |
| type 1 diabetes | phenotype |
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| Genetic Overlap Between Attention-Deficit/Hyperactivity Disorder and Bipolar Disorder: Evidence From Genome-wide Association Study Meta-analysis. | van Hulzen KJE et al. | β | 2017 | β |
| Genetic variation at the microRNA binding site of CAV1 gene is associated with lung cancer susceptibility. | Fang X et al. | β | 2017 | β |
| Genome-scale identification of microRNA-related SNPs associated with risk of head and neck squamous cell carcinoma. | Wilkins OM et al. | β | 2017 | β |
| Genome-Wide Prioritization and Transcriptomics Reveal Novel Signatures Associated With Thiazide Diuretics Blood Pressure Response. | Shahin MH et al. | β | 2017 | β |
| <i>In silico</i> analysis of single nucleotide polymorphisms (SNPs) in human FOXC2 gene. | Nimir M et al. | β | 2017 | β |
| MicroRNAs as biomarkers for psychiatric disorders with a focus on autism spectrum disorder: Current progress in genetic association studies, expression profiling, and translational research. | Hu Y et al. | β | 2017 | β |
| miRNA-Related Polymorphisms in miR-423 (rs6505162) and PEX6 (rs1129186) and Risk of Esophageal Squamous Cell Carcinoma in an Iranian Cohort. | Nariman-Saleh-Fam Z et al. | β | 2017 | β |
| miRNAs target databases: developmental methods and target identification techniques with functional annotations. | Singh NK | β | 2017 | β |
| Phenotype prediction for mucopolysaccharidosis type I by in silico analysis. | Ou L et al. | β | 2017 | β |
| Significance of functional disease-causal/susceptible variants identified by whole-genome analyses for the understanding of human diseases. | Hitomi Y et al. | β | 2017 | β |
| SNPs in microRNA target sites and their potential role in human disease. | MoszyΕska A et al. | β | 2017 | β |
| Structure and functional impact of seed region variant in MIR-499 gene family in bronchial asthma. | Toraih EA et al. | β | 2017 | β |
| Systematic Prediction of the Impacts of Mutations in MicroRNA Seed Sequences. | Bhattacharya A et al. | β | 2017 | β |
| The correlation between CRB1 variants and the clinical severity of Brazilian patients with different inherited retinal dystrophy phenotypes. | Motta FL et al. | β | 2017 | β |
| A 3'UTR polymorphism marks differential KLRG1 mRNA levels through disruption of a miR-584-5p binding site and associates with pemphigus foliaceus susceptibility. | Cipolla GA et al. | β | 2016 | β |
| A Bioinformatics Approach to Prioritize Single Nucleotide Polymorphisms in TLRs Signaling Pathway Genes. | Alipoor B et al. | β | 2016 | β |
| A Bioinformatics Approach to the Identification of Variants Associated with Type 1 and Type 2 Diabetes Mellitus that Reside in Functionally Validated miRNAs Binding Sites. | Ghaedi H et al. | β | 2016 | β |
| A comprehensive in silico analysis of non-synonymous and regulatory SNPs of human MBL2 gene. | Kalia N et al. | β | 2016 | β |
| A cross-ethnic survey of CFB and SLC44A4, Indian ulcerative colitis GWAS hits, underscores their potential role in disease susceptibility. | Gupta A et al. | β | 2016 | β |
| A genetic variation in microRNA target site of ETS2 is associated with clinical outcomes of paclitaxel-cisplatin chemotherapy in non-small cell lung cancer. | Hong MJ et al. | β | 2016 | β |
| Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection. | Pandey R et al. | β | 2016 | β |
| Association between CYP2E1 polymorphisms and risk of differentiated thyroid carcinoma. | PellΓ© L et al. | β | 2016 | β |
| Bioinformatics Approach for Prediction of Functional Coding/Noncoding Simple Polymorphisms (SNPs/Indels) in Human BRAF Gene. | Hassan MM et al. | β | 2016 | β |
| Bioinformatic tools for microRNA dissection. | Akhtar MM et al. | β | 2016 | β |
| Cis-acting single nucleotide polymorphisms alter MicroRNA-mediated regulation of human brain-expressed transcripts. | Ramachandran S et al. | β | 2016 | β |
| dbDSM: a manually curated database for deleterious synonymous mutations. | Wen P et al. | β | 2016 | β |
| Differential gene expression levels might explain association of LAIR2 polymorphisms with pemphigus. | Camargo CM et al. | β | 2016 | β |
| Double-strand break repair and colorectal cancer: gene variants within 3' UTRs and microRNAs binding as modulators of cancer risk and clinical outcome. | Naccarati A et al. | β | 2016 | β |
| Genetic variants of MAOB affect serotonin level and specific behavioral attributes to increase autism spectrum disorder (ASD) susceptibility in males. | Chakraborti B et al. | β | 2016 | β |
| Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types. | Kar SP et al. | β | 2016 | β |
| Genomic variations in non-coding RNAs: Structure, function and regulation. | Bhartiya D et al. | β | 2016 | β |
| GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. | Li MJ et al. | β | 2016 | β |
| Identification of critical variants within SLC44A4, an ulcerative colitis susceptibility gene identified in a GWAS in north Indians. | Gupta A et al. | β | 2016 | β |
| In silico analysis of deleterious single nucleotide polymorphisms in human BUB1 mitotic checkpoint serine/threonine kinase B gene. | Akhoundi F et al. | β | 2016 | β |
| In silico dissection of miRNA targetome polymorphisms and their role in regulating miRNA-mediated gene expression in esophageal cancer. | Nariman-Saleh-Fam Z et al. | β | 2016 | β |
| Interaction Between Peroxisome Proliferator Activated Receptor Ξ΄ and Epithelial Membrane Protein 2 Polymorphisms Influences HDL-C Levels in the Chinese Population. | Ke T et al. | β | 2016 | β |
| microRNA editing in seed region aligns with cellular changes in hypoxic conditions. | Nigita G et al. | β | 2016 | β |
| MicroRNA-related polymorphisms and non-Hodgkin lymphoma susceptibility in the Multicenter AIDS Cohort Study. | Peckham-Gregory EC et al. | β | 2016 | β |
| Mining of single nucleotide polymorphisms in the 3' untranslated region of liver cancer-implicated miR-122 target genes. | Suresh PS et al. | β | 2016 | β |
| MiRNA-Related Polymorphisms in miR-146a and TCF21 Are Associated with Increased Susceptibility to Coronary Artery Disease in an Iranian Population. | Bastami M et al. | β | 2016 | β |
| miRVaS: a tool to predict the impact of genetic variants on miRNAs. | Cammaerts S et al. | β | 2016 | β |
| Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges. | Veneziano D et al. | β | 2016 | β |
| Polymorphisms Falling Within Putative miRNA Target Sites in the 3'UTR Region of SIRT2 and DRD2 Genes Are Correlated With Human Longevity. | Crocco P et al. | β | 2016 | β |
| Reciprocal regulation between mRNA and microRNA enables a bistable switch that directs cell fate decisions. | Tian XJ et al. | β | 2016 | β |
| Separating the wheat from the chaff: systematic identification of functionally relevant noncoding variants in ADHD. | Tong JH et al. | β | 2016 | β |
| SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions. | Bhattacharya A et al. | β | 2016 | β |
| The miRNA targetome of coronary artery disease is perturbed by functional polymorphisms identified and prioritized by in-depth bioinformatics analyses exploiting genome-wide association studies. | Bastami M et al. | β | 2016 | β |
| Altered Gene Expression Associated with microRNA Binding Site Polymorphisms. | VΓ΅sa U et al. | β | 2015 | β |
| An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools. | Gong J et al. | β | 2015 | β |
| Bioinformatics prioritization of SNPs perturbing microRNA regulation of hematological malignancy-implicated genes. | Ghaedi H et al. | β | 2015 | β |
| Bioinformatics Resources for MicroRNA Discovery. | Moore AC et al. | β | 2015 | β |
| Biological databases for human research. | Zou D et al. | β | 2015 | β |
| Current trend of annotating single nucleotide variation in humans--A case study on SNVrap. | Li MJ et al. | β | 2015 | β |
| Genetic variability of microRNA regulome in human. | Obsteter J et al. | β | 2015 | β |
| Genetic variants in microRNA genes: impact on microRNA expression, function, and disease. | Cammaerts S et al. | β | 2015 | β |
| Genomic alterations as mediators of miRNA dysregulation in ovarian cancer. | Kan CW et al. | β | 2015 | β |
| Heterogeneity and individuality: microRNAs in mental disorders. | Hommers LG et al. | β | 2015 | β |
| In-silico QTL mapping of postpubertal mammary ductal development in the mouse uncovers potential human breast cancer risk loci. | Hadsell DL et al. | β | 2015 | β |
| Knowledge-based analysis of functional impacts of mutations in microRNA seed regions. | Bhattacharya A et al. | β | 2015 | β |
| lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. | Gong J et al. | β | 2015 | β |
| MicroRNA hsa-miR-4717-5p regulates RGS2 and may be a risk factor for anxiety-related traits. | Hommers L et al. | β | 2015 | β |
| microRNAs as pharmacogenomic biomarkers for drug efficacy and drug safety assessment. | Koturbash I et al. | β | 2015 | β |
| miR2GO: comparative functional analysis for microRNAs. | Bhattacharya A et al. | β | 2015 | β |
| Multi-ethnic analysis reveals soluble L-selectin may be post-transcriptionally regulated by 3'UTR polymorphism: the Multi-Ethnic Study of Atherosclerosis (MESA). | Berardi C et al. | β | 2015 | β |
| Overview of microRNA biology. | Mohr AM et al. | β | 2015 | β |
| Polymorphism in microRNA-binding site in HNF1B influences the susceptibility of type 2 diabetes mellitus: a population based case-control study. | Goda N et al. | β | 2015 | β |
| Polymorphisms in HLA-DPB1 are associated with differences in rubella virus-specific humoral immunity after vaccination. | Lambert ND et al. | β | 2015 | β |
| Post-Transcriptional Regulation of Renalase Gene by miR-29 and miR-146 MicroRNAs: Implications for Cardiometabolic Disorders. | Kalyani A et al. | β | 2015 | β |
| The genetics of human autoimmune disease: A perspective on progress in the field and future directions. | Seldin MF | β | 2015 | β |
| CardioGxE, a catalog of gene-environment interactions for cardiometabolic traits. | Parnell LD et al. | β | 2014 | β |
| Computational analysis of functional single nucleotide polymorphisms associated with the CYP11B2 gene. | Jia M et al. | β | 2014 | β |
| Computational prediction of disease microRNAs in domestic animals. | Buza T et al. | β | 2014 | β |
| CREAM: a database for chemotherapy resistance-associated miRSNP. | Dai E et al. | β | 2014 | β |
| Depression and BMI influences the serum vascular endothelial growth factor level. | Elfving B et al. | β | 2014 | β |
| Genetic variants in let-7/Lin28 modulate the risk of oral cavity cancer in a Chinese Han population. | Zhang Y et al. | β | 2014 | β |
| Genetic variation in the 3'-UTR of CYP1A2, CYP2B6, CYP2D6, CYP3A4, NR1I2, and UGT2B7: potential effects on regulation by microRNA and pharmacogenomics relevance. | Swart M et al. | β | 2014 | β |
| Inflammation-related genetic variants predict toxicity following definitive radiotherapy for lung cancer. | Pu X et al. | β | 2014 | β |
| In silico mapping of polymorphic miRNA-mRNA interactions in autoimmune thyroid diseases. | Cui Y | β | 2014 | β |
| miR-485-5p binding site SNP rs8752 in HPGD gene is associated with breast cancer risk. | He N et al. | β | 2014 | β |
| Polymorphism in miRNA-1 target site and circulating miRNA-1 phenotype are associated with the decreased risk and prognosis of coronary artery disease. | Wang L et al. | β | 2014 | β |
| Single-Nucleotide Polymorphisms Within MicroRNAs Sequences and Their 3' UTR Target Sites May Regulate Gene Expression in Gastrointestinal Tract Cancers. | Saadatian Z et al. | β | 2014 | β |