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https://sq-96.github.io/multigroup_ctwas_analysis/realdata_final_multigroup_summary.html
LDLR, PCSK9, CETP, CCNJ, PKN3, APOC1, ABCA8, FCGRT, DNAJC13, LRCH4, HMGCR, ASGR1, APOB, FLT3, ADH1B, ZDHHC18, USP39, TIMD4, ZFYVE1, NPC1L1, ERGIC3, ACP6, MITF, PSRC1, SNX17, GABBR1, KIF13B, R3HDM2, SIPA1, FAM117B, PGS1, MYPOP, USP3, ADRB1, WASHC4, PHC1, TPD52, THOP1, ZFP28, PDE4C, XPNPEP3, DMTN, SEPT2
Genes with Strong Evidence of Association with LDL Cholesterol
LDLR (Low-Density Lipoprotein Receptor): Mutations in LDLR are a primary cause of familial hypercholesterolemia, leading to elevated LDL cholesterol levels due to impaired clearance of LDL particles from the bloodstream. PCSK9 (Proprotein Convertase Subtilisin/Kexin Type 9): PCSK9 regulates LDL receptor degradation. Gain-of-function mutations increase LDL cholesterol levels, while loss-of-function mutations are associated with reduced LDL cholesterol and a lower risk of coronary heart disease.
file_path <- "figures/lz/LDL-ukb-d-30780_irnt/multi/LDLR.pdf"
cat("File exists:", file.exists(file_path), "\n")File exists: TRUE cat("Full path:", normalizePath(file_path))Full path: /project/xinhe/xsun/website/multigroup_ctwas_analysis/figures/lz/LDL-ukb-d-30780_irnt/multi/LDLR.pdfAPOB (Apolipoprotein B): APOB encodes the primary protein component of LDL particles. Mutations can impair LDL binding to its receptor, resulting in elevated LDL cholesterol levels.
CETP (Cholesteryl Ester Transfer Protein): CETP facilitates the transfer of cholesteryl esters from HDL to LDL and VLDL particles. Variants in CETP can influence HDL and LDL cholesterol levels. HMGCR (3-Hydroxy-3-Methylglutaryl-CoA Reductase): This enzyme is the rate-limiting step in cholesterol biosynthesis and is the target of statin therapy. Variants in HMGCR can affect LDL cholesterol levels. NPC1L1 (Niemann-Pick C1-Like 1): NPC1L1 is critical for intestinal cholesterol absorption. Inhibitors like ezetimibe target this protein to reduce LDL cholesterol levels. ASGR1 (Asialoglycoprotein Receptor 1): Loss-of-function mutations in ASGR1 have been associated with reduced LDL cholesterol levels and a lower risk of coronary artery disease. APOC1 (Apolipoprotein C1): APOC1 modulates lipoprotein metabolism and has been linked to variations in LDL cholesterol levels. PSRC1 (Proline and Serine Rich Coiled-Coil 1): Variants near PSRC1 have been linked to LDL cholesterol levels in genome-wide association studies (GWAS). TIMD4 (T-cell Immunoglobulin and Mucin Domain Containing 4): Variants in TIMD4 have been associated with decreased serum triglyceride levels and a reduced risk of coronary heart disease and ischemic stroke in certain populations.
sessionInfo()R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.12 rstudioapi_0.13 knitr_1.39 magrittr_2.0.3
[5] workflowr_1.7.0 R6_2.5.1 rlang_1.1.2 fastmap_1.1.0
[9] fansi_1.0.3 highr_0.9 stringr_1.5.1 tools_4.2.0
[13] xfun_0.41 utf8_1.2.2 cli_3.6.1 git2r_0.30.1
[17] jquerylib_0.1.4 htmltools_0.5.2 rprojroot_2.0.3 yaml_2.3.5
[21] digest_0.6.29 tibble_3.2.1 lifecycle_1.0.4 later_1.3.0
[25] sass_0.4.1 vctrs_0.6.5 promises_1.2.0.1 fs_1.5.2
[29] glue_1.6.2 evaluate_0.15 rmarkdown_2.25 stringi_1.7.6
[33] bslib_0.3.1 compiler_4.2.0 pillar_1.9.0 jsonlite_1.8.0
[37] httpuv_1.6.5 pkgconfig_2.0.3