. 2016 Oct 5;45(Database issue):D104–D114. doi: 10.1093/nar/gkw888

Table 1. Overview of data curated in POSTAR.

	Category	Human	Mouse	Resource/calculation method^a
RBP binding sites	RBP binding sites from experiments	1 752 329	1 003 984	All CLIP-seq peaks called by Piranha (human: 65 RBPs; mouse: 30 RBPs)^b
		39 201	78 922	HITS-CLIP peaks called by CIMS (human: 17 RBPs; mouse: 23 RBPs)^b
		7 731 846	96 346	PAR-CLIP peaks called by PARalyzer (human: 44 RBPs; mouse: 4 RBPs)^b
		4 598 307	1 013 008	iCLIP peaks called by CITS (human: 9 RBPs; mouse: 8 RBPs)^b
		6 703 559	NA	eCLIP-seq peaks called by ENCODE (human: 56 RBPs)^c
		439 817	NA	PIP-seq peaks called by PMID24393486 (human: global RBPs)
	RBP binding site from predictions	25 623 567	18 540 386	Peaks predicted by FIMO (human: 88 RBPs; mouse: 88 RBPs)^d
		19 447 967	24 621 203	Peaks predicted by TESS (human: 88 RBPs; mouse: 88 RBPs)^d
		16 586 127	11 905 150	Peaks predicted by DeepBind (human: 82 RBPs; mouse: 82 RBPs)^e
Data module I: Gene/RBP annotations	RBPs	132	104	Ensembl, PMID25365966
	Sequence motifs	726	180	MEME, HOMER
	Structural preferences	720	179	RNApromo, RNAcontext
	Gene Ontologies	15 677	13 849	GOBP, GOMF, GOCC^f
	Biological pathways	186	105	KEGG
	Gene expression	34 cells/tissue types	18 cell/tissue types	TopHat, Cufflinks^g
	Alternative splicing (skip exon)	34 cells/tissue types	18 cell/tissue types	TopHat, MISO^g
Data module II: Molecular annotations	miRNA binding sites from experiments	3 906 955	1 588 861	AGO CLIP-seq peaks called by Piranha, the targeting miRNAs identified by miRanda^h
	miRNA binding sites from predictions	70 516 087	38 336 372	RNAhybrid, TargetScan, miRanda
	RNA modification sites	177 049	91 930	RMBase, PMID26863196
	RNA editing sites	2 583 302	8846	RADAR, DARNED
	Splicing elements	1 995 574	1 152 186	Anno. in GENCODE human v19, mouse vM7
	Conserved structural regions	725	691	EvoFam
Data module III: Genomic variants	SNPs	149 398 310	77 785 586	dbSNP v146
	Tissue-specific eQTL	19 530 607	NA	GTEx
	GWAS SNPs	278 473	NA	GWASdb2, RNAfoldⁱ
	Clinically important SNPs	131 919	NA	ClinVar, RNAfoldⁱ
	Cancer TCGA whole-exome SNVs	828 119	NA	PMID24390350, RNAfoldⁱ
	Cancer TCGA whole-genome SNVs	4 745 891	NA	PMID23945592, RNAfoldⁱ
	Cancer COSMIC SNVs	2 371 219	NA	COSMIC v76, RNAfoldⁱ
Data module IV: Gene-Function associations	Tissue-specific genes	21 549	NA	TiGER, SpeCond
	Gene-Disease associations	419 906	NA	OMIM, DisGeNET
	Gene-Cancer associations	4485	NA	Manually curated from 60 publications^j
	Gene-Drug associations	35 201	NA	DGIdb 2.0
Data module V: RNA secondary structures	Predicted local structures	82 242 543	57 095 233	RNAfold with restraints from experimental structural probing data (human: DMS-seq, PARS; mouse: icSHAPE, Frag-seq, CIRS-seq)^k

^aResults and data firstly generated by POSTAR are in bold font.

^bWe provide all CLIP-seq peaks called by Piranha with P < 0.01. For CIMS, CITS and PARalyzer, we provide peaks with default significance cutoffs.

^cSee Supplementary File 2 for the full list of eCLIP-seq data. The peaks were called by ENCODE.

^dSee Supplementary File 5 for the RBPs and motifs used for prediction.

^eSee Supplementary File 6 for the RBPs in DeepBind model.

^fBP, Biological Process; MF, Molecular Function; CC, Cellular Component.

^gSee Supplementary File 4 for the full list of 230 RNA-seq data sets in human and mouse.

^hWe used all AGO CLIP-seq peaks called by Piranha (P < 0.01). The targeting miRNAs of the peaks were identified using miRanda with default parameters.

ⁱWe used RNAfold to calculate the minimal free energy changes of local RNA secondary structures that are induced by the mutations.

^jSee Supplementary File 3 for the full list of manually curated cancer genes.

^kSee Supplementary File 7 for the experimental structural probing datasets. We predicted one local structure centered on each RBP binding site (window size: 150nt).