Table 2.

A comparison of PlantPAN 3.0 with previous version and similar resources

	PlantPAN 3.0	PlantPAN 2.0a	PlantTFDB 4.0b	ChIPBase v2.0c	Expressod	ReMap 2018e	PCSDf
Number of species in this databases	78	76	165	10	1	1	3
Number of TFs	17 230	16 960	320 370	26	20	NAg	46
Number of TF matrices	4 703	1143	674	NAg (∼6 200)h	0	0	0
Number of plant species in ChIP-seq datasets	7	0	2	1	1	0	3
Number of regulatory factors in ChIP-seq datasets	99	0	14	29 (1414)h	20	0 (485)h	110
Number of ChIP-seq samples	662	0	NA	NA	NA	NA	NA
Number of ChIP-seq datasets	421	0	26	54 i (10 216)h	20	0 (2 829)h	303
Annotation of Target genes	Yes	Yes	No	Yes	Yes	No	Yes
Histon/Nuclesome Binding regions	Yes	No	Yes	Yes	No	Yes	Yes
Genome Browse for binding regions	Yes	No	Yes	Yes i	No	Yes	Yes
Uniform ChIP-seq data processing	Yes	No	Yes	No	No	Yes	Yes
Download whole genomic binding peaks (bed/bigwig files)	Yes	No	No	No	No	Yes	Yes
Comprehensive curation of TF information (i.e. functional domain, response conditions, target genes, activator or repressor, and sequence logos of binding motifs)	Yes (increase secondary and 3D structures, PTM, and variants)	Yes	Yes	No	No	No	No
Co-expression profiles of TFs and their target genes	Yes	Yes	No	Yes	Yes	No	No
Cis-regulatory element prediction	Yes	Yes	Yes	No	No	No	No

^aPlantPAN 2.0: http://PlantPAN2.itps.ncku.edu.tw/ (29).

^bPlantTFDB 4.0: http://planttfdb.cbi.pku.edu.cn/ (8).

^cChIPBase v2.0: http://rna.sysu.edu.cn/chipbase/ (9).

^dExpresso: http://bioinformatics.cs.vt.edu/expresso/ (10).

^eReMap 2018: http://remap.cisreg.eu (5).

^fPCSD: http://systemsbiology.cau.edu.cn/chromstates (51).

^gEach TF/matrices can be accessed from the database separately. However, the total number of TFs/matrices cannot be calculated via the resource.

^hThe number of data for plant species is shown without brackets, whereas the total number of data for plant and non-plant species is indicated within brackets.

ⁱRecently, this function/resource has not been available on the website (http://rna.sysu.edu.cn/chipbase/).