Table 1.

Comparison of accessibility information in ATACdb with other databases

Function type	Data type/Specific function	ATACdb	Cistrome	TCGA	ENCODE
Quality control	Mean insert size	✓
	Standard deviation	✓
	TSS enrichment score	✓			✓
	Fraction of reads in peaks	✓			✓
	Diagnostic plot a	✓	✓
TF footprint	Tag Count b	✓
	TF protection score c	✓
	Number of binding sites	✓
	Footprint logo	✓
Annotation	Strategies of accessible chromatin region associated genes d	3 e	1 f
	Common SNP	✓
	Risk SNP	✓
	eQTL	✓
	LD SNP	✓
	Super-enhancer	✓
	Enhancer	✓
	Methylation site	✓
	Chromatin interaction	✓
	TAD	✓
Peak annotation visualization	Genomic feature distribution	✓
	Peak relative to TSS distribution	✓
Genome browser	Accessible chromatin region	✓	✓
	SNP	✓
	Common SNP	✓
	Risk SNP	✓
	Super-enhancer	✓	✓
	Enhancer	✓
	TFBS conserved	✓
	TAD	✓
Analysis functions	Differential-Overlapping-Region analysis g	✓
	Overlapping accessible chromatin regions bound by two TFs analysis h	✓
Data browse	Simple information browse	✓	✓	✓	✓
	Browse based on samples classification i	✓
	Region statistics for each sample	✓
	Alphanumerically sortable table	✓

^aInsert size distribution plot.

^bNumber of reads around TFBSs used to rank footprint predictions.

^cFootprints with potentially short residence times.

^dAccessible chromatin region associated genes obtained by different strategies or algorithms.

^eClosest, overlap and proximal genes were identified by ROSE_geneMapper.

^fPutative targets were identified by BETA.

^gAnalyze differential and overlapping accessible chromatin regions.

^hAnalyze overlapping accessible chromatin regions bound by two TFs.

ⁱClassification of samples including Biosample type, Tissue type, Cancer type and Biosample name.