Introductions of moloc

Usage of search query  

Under "Search moloc" menu, please choose the region information that you want to query. If special methylation ID is known, for instance cg00000658, then you can query the database according to the ID.

• On the returned result table, if users click on the 'Gene ID', then another table will show up, which contains the information of the gene including all methylations that relate to the gene. Also, if users click on the 'Methylation ID' in the table, the information of that methylation including all genes relating to it will display.

• On all of the returned query result pages, user can click on the gene name to find more information about the gene through the GeneCards website.

For better webpage interface, please use Chrome or Firefox.

 

Result format  

Query results can be exported to a TAB-delimited format table.

• Users can download the 'main result table' via the link provided on main webpage (Downloads).

• Meaning of each column in the exported result table as well as the 'main result table' are described in the following.

 

Description of main table  

Meaning of each column in the main table is described as following:

• "id": unique Gene-Methylation Probe;

• "EnsembleID": Ensemble ID of the gene;

• "ProbeIDmet": methylation Probe ID;

• "Chr", "pos_start", "pos_end": cis-region considered in the analysis;

• "Gene_name": HGNC symbol of the gene if there is one;

• "geneChr, "geneStart", "geneStop", "geneStrand": gene position and strand information;

• "methChr", "methPos" : methylation Probe Position;

• "distMethylGeneTSS": distance between the methylation Probe and the TSS of the gene;

• "PGC2_LDclump": whether the region considered intersects with an LD block for SCZ as defined by the PGC2 consortium;

• "anneal_rank": SCZ LD block as defined by the PGC2 consortium;

• "PGC2_LDclump_info": position of the SCZ LD block;

• "nsnps": number of SNPs considered in the region;

• "bf_E", "bf_E_G" .. "bf_zero": Bayes Factors supporting respective hypotheses for the region;

• "PPA_E", "PPA_E_G".. "PPA_zero": Posterior Probabilities supporting respective hypotheses for the region;

• "bestSNP_PPA_biom_eqtl_methyl": This column contains the posterior probability for the SNP that has the highest probability of co-localization for each trait with any other trait;

• "bestSNP_biom": SNP with the highest posterior probability of GWAS co-localization with eQTL or mQTL (i.e. highest PPA of EG + EG.M + EM + EM.G + EGM);

• "bestSNP_eqtl": SNP with the highest posterior probability of eQTL co-localization with GWAS or mQTL (i.e. highest PPA of EG + EG.M + EM + EM.G + EGM);

• "bestSNP_methyl": SNP with the highest posterior probability of mQTL co-localization with GWAS or eQTL (i.e. highest PPA of GM + E.GM + E.GM + EM.G + EM + EGM);

• Columns begin with "bestSNP_BETA_biom": info and summary statistics for the best co-localizing SNP in each of the three traits;

• Columns begin with "minpiSNP_": info and summary statistics for the SNP with the lowest p-value in the region for each trait;

• Columns begin with "bestsnpGWAS_": info and summary statistics for the SNP reported by the PGC2 consortium as the index GWAS SCZ SNP, if the region intersects a SCZ LD block.

 

Citation  

If you use the moloc database in your research, please cite our paper:

C. Giambartolomei, J. Z. Liu, W. Zhang, M. Hauberg, H. Shi, J. Boocock, J. Pickrell, A. Jaffe, the CommonMind Consortium, B. Pasaniuc, P. Roussos. A Bayesian Framework for Multiple Trait Colocalization From Summary Association Statistics. bioRxiv, 2017. DOI: https://doi.org/10.1101/155481.

 

Additional references  

• Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics (PLoS Genetics, 2014)

• Detection and interpretation of shared genetic influences on 42 human traits (Nature Genetics, 2016)


Any questions, please feel free to contact: clauFightSomeSpamdia.giambartolomei@gmail.com, weFightSomeSpamn.zhang1@mssm.edu, panaFightSomeSpamgiotis.roussos@mssm.edu.



«Back to query