1. What is GPSno?

GPSno is a database to provide a comprehensive resource of the genetic and pharmacogenomic landscape of snoRNAs for 29 human cancer types in TCGA with sample size larger than 50.

In GPSno, users can:

1) Browse or search SNPs to find cis- and trans- regulated snoRNAs in different cancer types;
2) Browse or search snoRNAs to find related SNPs in different cancer types;
3) Browse or search snoQTLs associated with patient survival in different cancer types;
4) Browse or search snoQTLs in GWAS LD regions and annotated these snoQTLs in different diseases;
5) Browse or search drug response-related snoRNAs in different cancer types.

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2. The analytic pipeline of genetic impact on snoRNA expression.

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3. The summary of data.

Cancer type No. of samples No. of snoRNAs No. of genotypes Cis Trans Survival-associated snoQTLs GWAS-related snoQTLs Drug response-related
pairs esnoRNAs snoQTLs pairs esnoRNAs snoQTLs pairs unique tag_SNP unique snoQTL sample size snoRNA-drug pairs
ACC 78 465 3 652 701 244 9 244 0 0 0 78 26 4 26 77 34
BLCA 397 411 4 221 213 2697 69 2681 1383 54 1045 141 1272 38 853 127 92
BRCA 1073 464 2 791 786 3752 146 3643 2192 105 1455 3 1562 62 982 942 5
CESC 290 400 4 417 705 2225 66 2224 1659 67 1300 149 1154 35 716 173 101
COAD 433 456 4 191 023 3246 89 3231 1111 39 821 0 1229 41 877 4 -
ESCA 184 401 4 541 112 1680 30 1679 1026 31 769 0 911 21 601 172 0
HNSC 521 415 4 311 502 4050 82 3906 1771 39 1237 0 1695 43 1061 0 -
KICH 66 391 3 871 603 417 10 417 0 0 0 0 69 3 69 0 -
KIRC 512 441 4 600 464 4465 86 4197 1779 51 1180 110 1640 54 1019 0 -
KIRP 289 424 4 948 299 2867 59 2851 1201 38 813 27 1037 27 647 51 114
LGG 511 423 4 662 087 3333 62 3322 1251 42 885 28 1392 42 973 70 324
LIHC 370 451 4 192 863 2059 85 1990 1066 41 738 21 1005 28 621 183 97
LUAD 512 453 4 416 162 4308 77 4035 1679 52 1106 422 1486 47 998 0 -
LUSC 475 446 3 811 695 3221 78 3194 1598 52 1243 0 1348/td> 39 927 0 -
MESO 87 414 4 861 983 927 15 927 441 10 336 0 435 6 233 0 -
OV 462 486 2 307 154 2299 159 2184 1509 88 887 45 1153 42 583 0 -
PAAD 178 398 5 061 023 2017 39 2017 884 25 562 3 1082 24 732 117 35
PCPG 178 401 4 804 919 1468 36 1462 377 17 328 30 343 16 287 176 791
PRAD 480 417 4 859 157 4114 64 4096 2199 63 1501 156 1818 47 1048 150 1419
READ 160 472 4 638 399 1540 34 1539 1033 39 750 215 793 20 477 0 -
SARC 245 388 4 263 388 1641 48 1638 830 34 571 309 829 21 529 229 264
SKCM 97 451 4 768 644 987 20 987 958 23 673 20 631 13 331 57 38
STAD 409 434 4 406 785 2420 50 2376 1281 48 922 0 1148 32 750 0 -
TGCT 150 472 4 893 554 1922 31 1922 1205 28 846 1 1024 25 638 148 7226
THCA 496 435 4 889 302 5322 92 5067 2247 60 1525 8 1948 50 1156 387 286
THYM 124 462 5 132 519 1675 30 1675 750 21 452 1 857 15 544 119 5043
UCEC 536 480 4 101 587 2826 81 2820 2079 71 1459 79 1410 46 837 7 -
UCS 56 450 4 008 108 227 8 227 0 0 0 0 1 1 1 57 1
UVM 80 420 4 778 965 1167 22 1167 871 20 634 0 497 12 240 77 523

4. The snoQTL boxplot and survival Kaplan-Meier plot.

snoQTL boxplot
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Boxplots represent the gene expression in individuals carrying homozygote AA, heterozygous Aa, and homozygote aa, respectively.

Kaplan-Meier plot
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Lines represent the survival curve for individuals carrying homozygote AA, heterozygousAa, and homozygote aa, respectively.

5. The identification of GWAS-related snoQTLs.

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). snoQTLs that overlapp with tagSNPs and/or linkage disequilibrium regions were extracted as GWAS-related snoQTLs.

6. Drug response-related snoRNA.

We acquired imputed drug response data of TCGA patients to explore the impact of snoRNA expression on drug response. Associations between standardized snoRNA expression and imputed drug response of cancer patients were analyzed using Pearson's correlation. Drug response-associated snoRNAs were defined as FDRs <0.05.