4.8 Article

ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases

Dandan Huang et al.

Summary: VannoPortal is a comprehensive variant annotation database that integrates extensive genomic/epigenomic data and commonly used annotation databases, with rich features and visualization tools to provide comprehensive and context-specific variant annotations for biologists and clinicians.

NUCLEIC ACIDS RESEARCH (2022)

Article Genetics & Heredity

Fuchs Endothelial Corneal Dystrophy associated risk variant, rs3768617 in LAMC1 shows allele specific binding of GFI1B

Maynak Chakraborty et al.

Summary: This study investigated the genetic and functional association of an intronic variant of LAMC1, rs3768617, with Fuchs endothelial corneal dystrophy (FECD) in the Indian population. The results showed a significant genetic association between rs3768617 and FECD, and suggested that this association is mediated by the transcription factor GFI1B. Functional studies also revealed the regulatory role of rs3768617 in FECD pathogenesis and the involvement of LAMC1 in this process.
Article Multidisciplinary Sciences

Systematic analysis of binding of transcription factors to noncoding variants

Jian Yan et al.

Summary: This study systematically assessed the binding of human transcription factors to noncoding variants using SNP-SELEX, revealing that position weight matrices lack predictive power and support vector machine with k-mers representation shows improved performance. Highly predictive models for 94 human transcription factors were reported, demonstrating their utility in genome-wide association studies and understanding of molecular pathways in human traits and diseases.

NATURE (2021)

Article Multidisciplinary Sciences

COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types

Benjamin J. Schmiedel et al.

Summary: The study assessed the effects of COVID-19-risk variants on gene expression in various immune cell types, highlighting their potential impact on immune cell function and severe disease. Through transcriptome-wide association study and colocalization analysis, specific immune cell types and putative causal genes influenced by COVID-19-risk variants were identified.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Landscape of allele-specific transcription factor binding in the human genome

Sergey Abramov et al.

Summary: Sequence variants in gene regulatory regions can alter gene expression, affecting disease susceptibility and progression. A meta-analysis of thousands of ChIP-Seq experiments identified more than 500 thousand allele-specific binding events in the human genome, potentially linked to medical relevant phenotypes.

NATURE COMMUNICATIONS (2021)

Article Genetics & Heredity

Association of CXCR6 with COVID-19 severity: delineating the host genetic factors in transcriptomic regulation

Yulin Dai et al.

Summary: COVID-19 primarily affects the respiratory system and severe symptoms may be associated with genetic variations. Studies have shown that the genes CXCR6 and CCR9 play a regulatory role in lung gene expression and are related to disease severity.

HUMAN GENETICS (2021)

Article Biochemistry & Molecular Biology

A Panel of rSNPs Demonstrating Allelic Asymmetry in Both ChIP-seq and RNA-seq Data and the Search for Their Phenotypic Outcomes through Analysis of DEGs

Elena E. Korbolina et al.

Summary: This study used RNA-seq and ChIP-seq data from PAECs to search for rSNPs, identifying 14,266 rSNPs associated with allele-specific binding and expression. Statistical methods were utilized to improve efficiency, with a portion of the identified rSNPs being linked to GWAS phenotypes and eQTLs.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Gastroenterology & Hepatology

A Crohn's Disease-associated IL2RA Enhancer Variant Determines the Balance of T Cell Immunity by Regulating Responsiveness to IL-2 Signalling

Rimma Goldberg et al.

Summary: The study reveals that IBD patients carrying the rs61839660 SNP show an enhanced T-eff immune phenotype with increased pro-inflammatory cytokine expression in response to IL-2 stimulation, while individuals with the TT genotype may exhibit a more active gut homing phenotype and reduced T cell clonal capacity.

JOURNAL OF CROHNS & COLITIS (2021)

Article Multidisciplinary Sciences

Mapping the human genetic architecture of COVID-19

Mari E. K. Niemi et al.

Summary: The genetic make-up of an individual plays a role in susceptibility and response to viral infections. A global network of researchers identified 13 significant genetic loci associated with SARS-CoV-2 infection and severe COVID-19 cases. Mendelian randomization analyses suggest a causal role for smoking and body-mass index in severe COVID-19. Collaboration among human genetics researchers has allowed for the discovery of novel host genetic factors linked to COVID-19.

NATURE (2021)

Article Immunology

Immune-Based Prediction of COVID-19 Severity and Chronicity Decoded Using Machine Learning

Bruce K. Patterson et al.

Summary: CCR5 and its ligands play a role in COVID-19 pathogenesis, with a focus on immune responses. Elevated B-cells and certain monocytic subsets were observed in COVID-19 patients, while certain T-cell subsets were decreased compared to healthy controls. Various cytokines showed significantly different levels in COVID-19 patients compared to healthy controls, indicating immune dysregulation in the disease process.

FRONTIERS IN IMMUNOLOGY (2021)

Article Immunology

CXCR6 regulates localization of tissue-resident memory CD8 T cells to the airways

Alexander N. Wein et al.

JOURNAL OF EXPERIMENTAL MEDICINE (2019)

Article Biochemistry & Molecular Biology

SNP2TFBS-a database of regulatory SNPs affecting predicted transcription factor binding site affinity

Sunil Kumar et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Valerie A. Schneider et al.

GENOME RESEARCH (2017)

Article Multidisciplinary Sciences

Fine-mapping inflammatory bowel disease loci to single-variant resolution

Hailiang Huang et al.

NATURE (2017)

Review Genetics & Heredity

10 Years of GWAS Discovery: Biology, Function, and Translation

Peter M. Visscher et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2017)

Article Biotechnology & Applied Microbiology

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Ines de Santiago et al.

GENOME BIOLOGY (2017)

Article Biochemical Research Methods

Approximately independent linkage disequilibrium blocks in human populations

Tomaz Berisa et al.

BIOINFORMATICS (2016)

Article Multidisciplinary Sciences

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

Jieming Chen et al.

NATURE COMMUNICATIONS (2016)

Article Biochemical Research Methods

Predicting effects of noncoding variants with deep learning-based sequence model

Jian Zhou et al.

NATURE METHODS (2015)

Article Multidisciplinary Sciences

Genetic and epigenetic fine mapping of causal autoimmune disease variants

Kyle Kai-How Farh et al.

NATURE (2015)

Article Biochemistry & Molecular Biology

Annotation of functional variation in personal genomes using RegulomeDB

Alan P. Boyle et al.

GENOME RESEARCH (2012)

Article Biotechnology & Applied Microbiology

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Alexandre Melnikov et al.

NATURE BIOTECHNOLOGY (2012)

Article Multidisciplinary Sciences

Complex effects of nucleotide variants in a mammalian cis-regulatory element

Jamie C. Kwasnieski et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

dbSNP: the NCBI database of genetic variation

ST Sherry et al.

NUCLEIC ACIDS RESEARCH (2001)