Genes identified by integrative analysis


Step1: Select an integrative method

SMR     Sherlock

Step2: Select a GWAS study

PGC2    CLOZUK

Step3: Select an eQTL dataset

GTEx 14 brain tissue eQTL data
GTEx v7 Brain Anterior cingulate cortex BA24 GTEx v7 Pituitary
GTEx v7 Brain Nucleus accumbens basal ganglia GTEx v7 Brain Cortex
GTEx v7 Brain Caudate basal ganglia GTEx v7 Brain Hippocampus
GTEx v7 Brain Cerebellar Hemisphere GTEx v7 Brain Hypothalamus
GTEx v7 Brain Putamen basal ganglia GTEx v7 Brain Amygdala
GTEx v7 Brain Spinal cord cervical GTEx v7 Brain Cerebellum
GTEx v7 Brain Frontal Cortex BA9 GTEx v7 Brain Substantia nigra
Other eQTL data
Westra peripheral blood CAGE peripheral blood
GTEx meta brain GTEx CMC ROSMAP
PsychENCODE Brain PFC
Example for Integrative method
SMR
Example for GWAS study
CLOZUK
Example for eQTL data
PsychENCODE

Step1: Select an integrative method

SMR     Sherlock

Step2: Select a GWAS study

PGC2    CLOZUK

Step3: Select an eQTL dataset

LBC BSGS meta ROSMAP Hannon Jaffe meta
Hannon Blood dataset1 Hannon Blood dataset2
Hannon Fetal Brain
Example for Integrative method
SMR
Example for GWAS study
CLOZUK
Example for eQTL data
ROSMAP Hannon Jaffe meta

References

SMR -Zhu et al. 2016. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nature Genetics, 48(5):481-487. [PMID: 27019110]
Sherlock -He et al. 2013. Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS. The American Journal of Human Genetics, 92(5):667–680. [PMID: 23643380]
PGC2 -Schizophrenia Working Group of the Psychiatric Genomics Consortium. 2014. Biological insights from 108 schizophrenia-associated genetic loci. Nature, 511(7510):421-427. [PMID: 25056061]
CLOZUK -Pardiñas et al. 2018. Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nature Genetics, 50(3):381-389. [PMID: 29483656]
GTEx -GTEx Consortium. 2013. The Genotype-Tissue Expression (GTEx) project. Nature Genetics, 45(6):580-585. [PMID: 23715323]
Westra eQTL -Westra et al. 2013. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nature Genetics, 45(10):1238-1243. [PMID: 24013639]
CAGE eQTL -Lloyd-Jones et al. 2017. The Genetic Architecture of Gene Expression in Peripheral Blood. The American Journal of Human Genetics, 100(2):371. [PMID: 28157541]
GTEx CMC ROSMAP -Qi et al. 2018. Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood. Nature Communications, 9(1):2282. [PMID: 29891976]
-GTEx Consortium. 2013. The Genotype-Tissue Expression (GTEx) project. Nature Genetics, 45(6):580-585. [PMID: 23715323]
-Fromer et al. 2016. Gene expression elucidates functional impact of polygenic risk for schizophrenia. Nature Neuroscience, 19(11):1442-1453. [PMID: 27668389]
-Ng et al. 2017. An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome. Nature Neuroscience, 20(10):1418-1426. [PMID: 28869584]
PsycheENCODE Brain PFC -Wang et al. 2018. Comprehensive functional genomic resource and integrative model for the human brain. Science, 362(6420), pii: eaat8464 [PMID: 30545857]
Myers Brain -Myers et al. 2009. A survey of genetic human cortical gene expression. Nature Genetics, 39(12):1494-1499. [PMID: 17982457]
LBC BSGS meta -McRae et al. 2018. Identification of 55,000 Replicated DNA Methylation QTL. Scientific Reports, 8(1):17605. [PMID: 30514905]
Hannon Blood eQTL -Hannon et al. 2016. An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation. Genome Biology, 17(1):176. [PMID: 27572077]
Hannon Fetal Brain -Hannon et al. 2016. Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. Nature Neuroscience, 19(1):48-54. [PMID: 26619357]
If you used the integrative analysis result in this database, please cite the relative references.