PMC:5118429 / 15755-17308
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/5118429","sourcedb":"PMC","sourceid":"5118429","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5118429","text":"The ssGWAS2 scenario described by Wang et al. (2014) was used to estimate genomic breeding values and iteratively estimate and weight SNP effects. Windows of 20 adjacent SNPs based on the new genetic linkage map were created using POSTGSF90 (Aguilar et al., 2014). Creation of windows of consecutive SNPs can capture the effect of the quantitative trait loci (QTL) better than a single SNP (Habier et al., 2011) due to signal concentration (Sun et al., 2011). Similar to previous reports (Dikmen et al., 2013; Fragomeni et al., 2014; Wang et al., 2014; Zhang et al., 2016), we found that the use of windows with a smaller number of SNPs resulted in a decreased signal-to-noise ratio compared to windows with 20 or more SNPs (data not shown). Therefore, exclusive windows (non-overlapping) of 20 consecutive SNPs were used in the GWAS analyses and the Manhattan plots with GWAS results were created using the R package qqman (Turner, 2014). Due to the quantitative nature of the traits used in this study, five iterations (wssGWAS) were implemented to reduce the background noise of SNP windows and differentiate the windows accounting for the largest proportion of variance. However, the differences in the results beyond 3 iterations were minimal (results not presented). Rather than using P-values from classical hypothesis tests to declare regions as significantly associated with the trait (Dikmen et al., 2013), here we identified genomic regions (windows) that explained the highest proportion (around 1%) of genetic variances (Wang et al., 2014).","tracks":[{"project":"2_test","denotations":[{"id":"27920797-24904635-33226441","span":{"begin":47,"end":51},"obj":"24904635"},{"id":"27920797-21605355-33226442","span":{"begin":406,"end":410},"obj":"21605355"},{"id":"27920797-21624169-33226443","span":{"begin":453,"end":457},"obj":"21624169"},{"id":"27920797-23935954-33226444","span":{"begin":504,"end":508},"obj":"23935954"},{"id":"27920797-25324857-33226445","span":{"begin":528,"end":532},"obj":"25324857"},{"id":"27920797-24904635-33226446","span":{"begin":547,"end":551},"obj":"24904635"},{"id":"27920797-27594861-33226447","span":{"begin":567,"end":571},"obj":"27594861"},{"id":"27920797-23935954-33226448","span":{"begin":1410,"end":1414},"obj":"23935954"},{"id":"27920797-24904635-33226449","span":{"begin":1547,"end":1551},"obj":"24904635"}],"attributes":[{"subj":"27920797-24904635-33226441","pred":"source","obj":"2_test"},{"subj":"27920797-21605355-33226442","pred":"source","obj":"2_test"},{"subj":"27920797-21624169-33226443","pred":"source","obj":"2_test"},{"subj":"27920797-23935954-33226444","pred":"source","obj":"2_test"},{"subj":"27920797-25324857-33226445","pred":"source","obj":"2_test"},{"subj":"27920797-24904635-33226446","pred":"source","obj":"2_test"},{"subj":"27920797-27594861-33226447","pred":"source","obj":"2_test"},{"subj":"27920797-23935954-33226448","pred":"source","obj":"2_test"},{"subj":"27920797-24904635-33226449","pred":"source","obj":"2_test"}]},{"project":"MyTest","denotations":[{"id":"27920797-24904635-33226441","span":{"begin":47,"end":51},"obj":"24904635"},{"id":"27920797-21605355-33226442","span":{"begin":406,"end":410},"obj":"21605355"},{"id":"27920797-21624169-33226443","span":{"begin":453,"end":457},"obj":"21624169"},{"id":"27920797-23935954-33226444","span":{"begin":504,"end":508},"obj":"23935954"},{"id":"27920797-25324857-33226445","span":{"begin":528,"end":532},"obj":"25324857"},{"id":"27920797-24904635-33226446","span":{"begin":547,"end":551},"obj":"24904635"},{"id":"27920797-27594861-33226447","span":{"begin":567,"end":571},"obj":"27594861"},{"id":"27920797-23935954-33226448","span":{"begin":1410,"end":1414},"obj":"23935954"},{"id":"27920797-24904635-33226449","span":{"begin":1547,"end":1551},"obj":"24904635"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"attributes":[{"subj":"27920797-24904635-33226441","pred":"source","obj":"MyTest"},{"subj":"27920797-21605355-33226442","pred":"source","obj":"MyTest"},{"subj":"27920797-21624169-33226443","pred":"source","obj":"MyTest"},{"subj":"27920797-23935954-33226444","pred":"source","obj":"MyTest"},{"subj":"27920797-25324857-33226445","pred":"source","obj":"MyTest"},{"subj":"27920797-24904635-33226446","pred":"source","obj":"MyTest"},{"subj":"27920797-27594861-33226447","pred":"source","obj":"MyTest"},{"subj":"27920797-23935954-33226448","pred":"source","obj":"MyTest"},{"subj":"27920797-24904635-33226449","pred":"source","obj":"MyTest"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ecaa93","default":true},{"id":"MyTest","color":"#9396ec"}]}]}}