Liverome: a curated database of liver cancer-related gene signatures with self-contained context information

Table 1 Comparison of Liverome with other related tools.

	Liverome	EHCO	dbDEPC	CCancer	GeneSigDB
Data coverage
Coverage of phenotype	HCC only	HCC only	15 cancers	Half the data are on cancer	Mostly cancer and stem cell
Coverage of HCC-specific data (signatures // articles)	143 // 98	12 // 32	6 // 5	25 // 21	34 // 18
Overall data coverage	Same as above	Same as above	65 // 48	3369 // 2644	2142 // 973
Covers both transcriptomics and proteomics studies	Yes	Yes	No (proteomics only)	Yes	Yes
Data content
Explicit designation of compared sample groups	Yes	No	Yes	No	No
Contains numerical ranking information	Yes	No (change direction only)	Yes (fold change only)	No	Yes
Uniform representation of numerical ranking values	Yes (unique to Liverome)	No	No	No	No
Informative naming of signatures	Yes (unique to Liverome)	No	No	No	No
Summary of experiment	Yes (unique to Liverome)	No	No	No	No
Web interface
Signature comparison tool	Yes	No	Yes	Yes	Yes
Gene search tool	Yes	Yes	Yes	No	Yes
Functional categorization of signatures for guided browsing	Yes (unique to Liverome)	No	No	No	No
Spreadsheet-like sorting utility for prioritization	Yes (unique to Liverome)	No	No	No	No

Liverome is compared to four other gene signature databases with respect to Liverome’s main utility as a gene search and signature comparison resource for liver cancer research community. Liverome achieves the largest coverage of HCC signatures and the most informative data content at the same time. Its web interface is designed to facilitate the retrieval of the informative data content, the guided browsing of signatures, and their comparison for occurrence-based prioritization.