Cross-species Conservation of context-specific networks

BMC Systems Biology

Table 1 Regulatory networks included in the croco-repo

Species	Global networks			Context-specific networks							\(\sum \)
	Databases	Literature	Binding site	ChIP				Open chromatin
	N	N	N	CO	AB	E	N	CO	E	N	N
Human	4	4	12	103	192	1,206	1,206	105	248	3,617	4,843
Mouse	2	4	12	28	50	162	162	39	123	1,800	1,980
Worm	2	4	4	15	91	561	561	—	—	–	575
Fly	3	4	22	23	59	119	119	—	—	–	148
\(\sum \)	11	16	54	169	392	2,048	2,048	144	371	5,417	7,546

Global networks and context-specific networks derived from the ENCODE data are integrated into the CroCo repository. Database derived networks stem from different curated sources (e.g., ORegAnno [39] and REDFly [40]). The binding site predicted networks result from different PWM collections and a sensitive and a specific PWM match threshold. Furthermore, four different global literature derived networks are included for each species. The majority of networks in the repository is inferred from context-specific ChIP and open chromatin experiments. In total, 2,048 networks derived from ChIP experiments performed for different antibodies and cell-lines are integrated into CroCo. Additionally, 5,417 networks derived from 371 open chromatin based experiments (e.g., DNase-seq and FAIRE-seq) are integrated into CroCo
N=Number of networks
CO=Number of different contexts (cell-lines for human, cell-lines or tissues for mouse, development stages for worm and fly)
AB=Number of different antibodies
E=Number of experiments

ISSN: 1752-0509