• 1. What is Pancan-meQTL?
  • 2. The pipeline of database construction.
  • 3. Data summary.
  • 4. The meQTL boxplot and survival Kaplan-Meier plot.
  • 5. The identification of GWAS-related meQTLs.
  • 6. Contact us.
    • Video tutorial
    1. What is Pancan-meQTL?

    Pancan-meQTL is a database to provide a comprehensive resource of methylation quantitative trait loci (meQTLs) for 23 human cancer types in TCGA with sample size larger than 100.

    In Pancan-meQTL, users can:

  • Browse or search cis-meQTLs and trans-meQTLs across different cancer types;
  • Browse or search meQTLs associated with patient survival across different cancer types;
  • Browse or search meQTLs in GWAS linkage disequilibrium (LD) regions;
    • 2. The pipeline of database construction
    cis
    3. Data summary
    Cancer type
    Full name
    No. of samples
    No. of methylaiton probes
    No. of genotypes
    Cis-pairs
    Cis-meProbes
    Cis-meQTLs
    Trans-pairs
    Trans-meProbes
    Trans-meQTLs
    BLCA Bladder Urothelial Carcinoma 405 384903 4182865 502774 8136 301392 216341 46165 51295
    BRCA Breast invasive carcinoma 664 384084 2721411 340881 7289 203391 47355 1804 31118
    CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma 290 383425 4289322 531458 11284 318082 212025 48741 46185
    CRC Colon adenocarcinoma + Rectum adenocarcinoma 354 380594 3879590 555556 10781 316517 185943 40872 55402
    ESCA Esophageal carcinoma 173 382712 4357977 408020 15726 260629 21790 5427 13297
    HNSC Head and Neck squamous cell carcinoma 501 385146 4245789 706915 10590 392427 100579 16599 51195
    KIRC Kidney renal clear cell carcinoma 306 384916 4487756 827668 14184 455287 598701 95277 82497
    KIRP Kidney renal papillary cell carcinoma 271 384786 4827856 830528 14986 486170 232041 52484 58017
    LAML Acute Myeloid Leukemia 122 385529 5121896 408043 10758 283314 22473 606 17201
    LGG Lower Grade Glioma 487 385198 4611830 789126 11092 454090 151792 24257 61737
    LIHC Liver hepatocellular carcinoma 367 383962 4152031 449509 9378 272962 127824 28610 46149
    LUAD Lung adenocarcinoma 448 384670 4343043 525439 8848 297745 110266 19790 52156
    LUSC Lung squamous cell carcinoma 359 385034 3676672 598237 10039 334937 191909 44240 60597
    PAAD Pancreatic adenocarcinoma 177 382517 4989296 903193 24432 513599 120777 41820 34727
    PCPG Pheochromocytoma and Paraganglioma 175 385235 4701955 589160 19388 385289 34905 2175 23719
    PRAD Prostate adenocarcinoma 479 385067 4801718 1129044 16366 574577 188046 46160 66084
    SARC Sarcoma 257 382095 4083674 458278 14059 287992 64709 22198 24734
    SKCM Skin Cutaneous Melanoma 103 384364 4838338 200763 6689 150232 8399 399 6332
    STAD Stomach adenocarcinoma 367 383290 4265676 687004 10723 382962 77711 9612 49489
    TGCT Testicular Germ Cell Tumors 148 385618 4807863 470576 14871 309018 36183 3791 25912
    THCA Thyroid carcinoma 498 385449 4842972 830377 11908 477575 248274 36261 72317
    THYM Thymoma 120 385609 4940146 562478 17015 352356 28228 1981 22009
    UCEC Uterine Corpus Endometrial Carcinoma 171 385407 4961809 314774 14181 218421 17953 2911 12881
    4. The meQTL boxplot and survival Kaplan-Meier plot.
    meQTL boxplot
    Kaplan-Meier plot

    Boxplots represent the methylation levers in individuals carrying homozygote AA, heterozygous Aa, and homozygote aa, respectively.

    Lines represent the survival curve for individuals carrying homozygote AA, heterozygous Aa, and homozygote aa, respectively.
    5. The identification of GWAS-related meQTLs

    GWAS tagSNPs were downloaded from GWAS catalog website (http://www.ebi.ac.uk/gwas/) and the GWAS linkage disequilibrium regions were extracted from SNAP database (https://personal.broadinstitute.org/plin/snap/ldsearch.php). meQTLs that overlapp with tagSNPs and/or linkage disequilibrium regions were extracted as GWAS-related meQTLs.

    6. Contact us
    Leng Han, Ph.D. Assistant Professor

    CPRIT (Cancer Prevention Research Institute of Texas) Scholar

    Email:   Leng Han

    Han Lab

    Department of Biochemistry & Molecular Biology

    The University of Texas Health Science Center at Houston, Houston, 77030 USA