Table 1.
Overview of data curated in POSTAR2
| Category | Human | Mouse | Fly | Worm | Arabidopsis | Yeast | Notes | |
|---|---|---|---|---|---|---|---|---|
| RBP-binding sites | RBP-binding sites from experiments | 3 759 076 | 1 193 757 | 97 322 | 35 652 | 31 183 | 324 641 | All CLIP-seq peaks called by Piranha |
| 75 734 | 110 876 | 1717 | 46 | 568 | 5800 | HITS-CLIP peaks called by CIMS | ||
| 15 788 784 | 226 458 | 417 150 | 29 784 | NA | 4 575 287 | PAR-CLIP peaks called by PARalyzer | ||
| 9 131 076 | 1 067 309 | 87 049 | 406 571 | 119 754 | NA | iCLIP peaks called by CITS | ||
| 2 436 040 | NA | NA | NA | NA | NA | eCLIP peaks called by ENCODE | ||
| 439 817 | NA | NA | NA | NA | NA | PIP-seq peaks called by PMID24393486 | ||
| RBP | RBPs | 171 | 39 | 5 | 5 | 2 | 62 | Ensembl, PMID25365966 |
| Sequence motifs | 1218 | 252 | 30 | 30 | 12 | 366 | MEME, HOMER | |
| Structural preferences | 1169 | 245 | 30 | 30 | 11 | 352 | RNApromo, RNAcontext | |
| Gene Ontologies | 108 787 | 41 501 | 2976 | 2145 | 1238 | 26 013 | GOBP, GOMF, GOCC | |
| RNA | Gene expression | 12 cell/tissue types | 10 cell/tissue types | 30 developmental stages | 35 developmental stages | 4 cell/tissue types | 3 conditions | GEO database Expression Atlas |
| miRNA-binding sites from experiments | 3 906 955 | 1 588 861 | NA | NA | NA | NA | AGO CLIP-seq peaks called by Piranha, the targeting miRNAs identified by miRanda | |
| miRNA-binding sites from predictions | 12 196 959 | 7 563 080 | 1 099 046 | 671 012 | 2524 | NA | miRanda, RNAhybrid, psRobot, psRNAtarget | |
| RNA modification sites | 489 629 | 495 232 | 6819 | NA | 20 331 | 71 466 | RMBase2, PMID26863196 | |
| RNA editing sites | 2 583 302 | 8846 | 5037 | 111 134 | NA | NA | RADAR, DARNED, PMID25373143 | |
| SNVs | 323 138 224 | 81 432 271 | 5 618 672 | 189 322 | 13 412 332 | 486 302 | dbSNP, PMID21079745 | |
| GWAS SNPs | 278 473 | NA | NA | NA | NA | NA | GWASdb2 | |
| Clinically important SNPs | 131 919 | NA | NA | NA | NA | NA | ClinVar | |
| Cancer TCGA whole-exome SNVs | 3 427 854 | NA | NA | NA | NA | NA | PMID29596782 | |
| Cancer TCGA whole-genome SNVs | 4 745 891 | NA | NA | NA | NA | NA | PMID23945592 | |
| Cancer COSMIC SNVs | 2 371 219 | NA | NA | NA | NA | NA | COSMIC | |
| Translatome | Condition | 17 cell/tissues types | 6 cell/tissue types | 5 stages/cell types | 3 cell types | 8 conditions | 6 conditions | GEO database |
| Annotated ORF | 65 319 | 38 686 | 30 357 | 20 108 | 26 916 | 6498 | ORFs annotated by reference | |
| Truncated ORF | 2 922 855 | 2 072 685 | 1 993 300 | 556 378 | 749 484 | 193 126 | ORFs with the same stop codon as aORF but downstream start codon | |
| Extended ORF | 102 866 | 3128 | 29 440 | 7840 | 11 673 | 0 | ORF with the same stop codon as aORF but upstream start codon | |
| Internal overlapped ORF | 2 828 307 | 1 973 410 | 1 490 433 | 704 924 | 983 723 | 193 982 | Off-frame ORFs that overlaps with aORF | |
| uORF | 413 508 | 226 589 | 273 310 | 14 460 | 48 784 | 0 | ORFs located upstream of aORF | |
| dORF | 3 266 469 | 1 921 443 | 551 813 | 51 642 | 141 319 | 0 | ORFs located downstream of aORF | |
| Unannotated ORF | 5 815 149 | 3 836 094 | 155 945 | 953 269 | 1 210 658 | 11 461 | ORFs with no annotation |