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Multi-tissue polygenic models for transcriptome-wide association studies

https://doi.org/10.1101/107623
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Psychotic Disorders and Sex Offending in a Danish Birth Cohort
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Schizophrenia, Substance Abuse, and Violent Crime
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Genome-Wide Association Studies of Alcohol Dependence and Substance Use Disorders
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Negotiating multicollinearity with spike-and-slab priors
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The Genetics of Alzheimer's Disease
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GCTA: A Tool for Genome-wide Complex Trait Analysis
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Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies
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Colocalization of GWAS and eQTL Signals Detects Target Genes
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Effects of aging on blood brain barrier and matrix metalloproteases following controlled cortical impact in mice
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What is an immunological synapse?
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Rapid stress-induced transcriptomic changes in the brain depend on beta-adrenergic signaling
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Amyloid-Beta-Activated Human Microglial Cells Through ER-Resident Proteins
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Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity
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Biological insights from 108 schizophrenia-associated genetic loci
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An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations
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Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease
inferredcites →https://doi.org/10.1038/ng.3367openalex-snapshot
A gene-based association method for mapping traits using reference transcriptome data
inferredcites →https://doi.org/10.1038/ng.3506openalex-snapshot
Integrative approaches for large-scale transcriptome-wide association studies
inferredcites →https://doi.org/10.1038/nmeth.2848openalex-snapshot
Efficient multivariate linear mixed model algorithms for genome-wide association studies
inferredcites →https://doi.org/10.1038/s41588-018-0268-8openalex-snapshot
Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions
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Effects of aging on circadian patterns of gene expression in the human prefrontal cortex
inferredcites →https://doi.org/10.1080/00031305.2015.1031827openalex-snapshot
Bayesian Variable Selection Under Collinearity
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Bayesian Variable Selection in Linear Regression
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PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R
inferredcites →https://doi.org/10.1093/biostatistics/kxw041openalex-snapshot
False discovery rates: a new deal
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1093/oxfordjournals.schbul.a033338openalex-snapshot
Schizophrenia, Alcohol Abuse, and Violent Behavior: A 26-Year Followup Study of an Unselected Birth Cohort
inferredcites →https://doi.org/10.1101/cshperspect.a006296openalex-snapshot
The Genetics of Alzheimer Disease
inferredcites →https://doi.org/10.1111/j.1440-1711.2005.01305.xopenalex-snapshot
Immune dysregulation and self‐reactivity in schizophrenia: Do some cases of schizophrenia have an autoimmune basis?
inferredcites →https://doi.org/10.1111/j.1467-9868.2005.00503.xopenalex-snapshot
Regularization and Variable Selection Via the Elastic Net
inferredcites →https://doi.org/10.1111/j.1530-0277.2010.01156.xopenalex-snapshot
Genome‐Wide Association Study of Alcohol Dependence Implicates a Region on Chromosome 11
inferredcites →https://doi.org/10.1111/j.2517-6161.1996.tb02080.xopenalex-snapshot
Regression Shrinkage and Selection Via the Lasso
inferredcites →https://doi.org/10.1126/science.1262110openalex-snapshot
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
inferredcites →https://doi.org/10.1186/1755-8794-1-44openalex-snapshot
A genome-wide association study for late-onset Alzheimer's disease using DNA pooling
inferredcites →https://doi.org/10.1186/gb-2014-15-1-r1openalex-snapshot
Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis
inferredcites →https://doi.org/10.1186/s12864-015-2159-zopenalex-snapshot
Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimer’s disease
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1192/bjp.bp.111.096321openalex-snapshot
Sleep and circadian rhythm disruption in schizophrenia
inferredcites →https://doi.org/10.1198/000313005x41337openalex-snapshot
Graphical Views of Suppression and Multicollinearity in Multiple Linear Regression
inferredcites →https://doi.org/10.1214/11-aoas455openalex-snapshot
Bayesian variable selection regression for genome-wide association studies and other large-scale problems
inferredcites →https://doi.org/10.1214/12-ba703openalex-snapshot
Scalable Variational Inference for Bayesian Variable Selection in Regression, and Its Accuracy in Genetic Association Studies
inferredcites →https://doi.org/10.1214/aos/1176344136openalex-snapshot
Estimating the Dimension of a Model
inferredcites →https://doi.org/10.1287/mnsc.24.2.210openalex-snapshot
Means and Variances of Stochastic Vector Products with Applications to Random Linear Models
inferredcites →https://doi.org/10.1371/journal.pgen.1003264openalex-snapshot
Polygenic Modeling with Bayesian Sparse Linear Mixed Models
inferredcites →https://doi.org/10.1371/journal.pgen.1003486openalex-snapshot
A Statistical Framework for Joint eQTL Analysis in Multiple Tissues
inferredcites →https://doi.org/10.1371/journal.pgen.1003649openalex-snapshot
Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs
inferredcites →https://doi.org/10.1371/journal.pgen.1003770openalex-snapshot
Integrated Enrichment Analysis of Variants and Pathways in Genome-Wide Association Studies Indicates Central Role for IL-2 Signaling Genes in Type 1 Diabetes, and Cytokine Signaling Genes in Crohn's Disease
inferredcites →https://doi.org/10.1371/journal.pgen.1004383openalex-snapshot
Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics
inferredcites →https://doi.org/10.1371/journal.pone.0092209openalex-snapshot
Area under Precision-Recall Curves for Weighted and Unweighted Data
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Overrepresentation of Glutamate Signaling in Alzheimer's Disease: Network-Based Pathway Enrichment Using Meta-Analysis of Genome-Wide Association Studies
inferredcites →https://doi.org/10.1523/jneurosci.4252-03.2004openalex-snapshot
Verge: A Novel Vascular Early Response Gene
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Regularization Paths for Generalized Linear Models via Coordinate Descent
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Uncoordinated 119 Protein Controls Trafficking of Lck via the Rab11 Endosome and Is Critical for Immunological Synapse Formation
inferredcites →https://doi.org/10.48550/arxiv.1206.6430openalex-snapshot
Variational Bayesian Inference with Stochastic Search
inferredcites →https://doi.org/10.48550/arxiv.1312.6114openalex-snapshot
Auto-Encoding Variational Bayes
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Stochastic variational inference
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Generalized spike-and-slab priors for Bayesian group feature selection using expectation propagation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/9781119487845.ch25openalex-snapshot
Inferring Causal Associations between Genes and Disease via the Mapping of Expression Quantitative Trait Loci
inferred← citeshttps://doi.org/10.1002/jcb.28744openalex-snapshot
Integrative analysis of transcriptome‐wide association study data and messenger RNA expression profiles identified candidate genes and pathways for inflammatory bowel disease
inferred← citeshttps://doi.org/10.1007/s40484-020-0207-4openalex-snapshot
Transcriptome‐wide association studies: a view from Mendelian randomization
inferred← citeshttps://doi.org/10.1016/j.euroneuro.2018.07.008openalex-snapshot
GENOME-WIDE ASSOCIATION STUDY IMPLICATES CHRNA2 IN CANNABIS USE DISORDER
inferred← citeshttps://doi.org/10.1016/j.psc.2018.10.007openalex-snapshot
Genetics of Eating Disorders
inferred← citeshttps://doi.org/10.1016/j.psychres.2019.112639openalex-snapshot
An integrative analysis of transcriptome-wide association study and mRNA expression profile identified candidate genes for attention-deficit/hyperactivity disorder
inferred← citeshttps://doi.org/10.1038/s41588-018-0148-2openalex-snapshot
Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits
inferred← citeshttps://doi.org/10.1093/hmg/ddab016openalex-snapshot
Multi-omics analyses of cognitive traits and psychiatric disorders highlight brain-dependent mechanisms
inferred← citeshttps://doi.org/10.1093/nar/gkaa767openalex-snapshot
A tissue-specific collaborative mixed model for jointly analyzing multiple tissues in transcriptome-wide association studies
inferred← citeshttps://doi.org/10.1101/219428openalex-snapshot
A Bayesian approach to mediation analysis predicts 206 causal target genes in Alzheimer’s disease
inferred← citeshttps://doi.org/10.1101/531673openalex-snapshot
A causal inference framework for estimating genetic variance and pleiotropy from GWAS summary data
inferred← citeshttps://doi.org/10.1186/s13040-024-00385-xopenalex-snapshot
The goldmine of GWAS summary statistics: a systematic review of methods and tools
inferred← citeshttps://doi.org/10.15302/j-qb-020-0228openalex-snapshot
Transcriptome wide association studies: general framework and methods
inferred← citeshttps://doi.org/10.1534/genetics.117.300270openalex-snapshot
A Powerful Framework for Integrating eQTL and GWAS Summary Data
inferred← citeshttps://doi.org/10.70675/061da45czf5e5z482dzb71dz92b95c997a05openalex-snapshot
Dissecting human population variation in single-cell responses to SARS-CoV-2
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The missing link between genetic association and regulatory function
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