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.

Lee et al. BMC Genomics 2011 12(Suppl 3):S3   doi:10.1186/1471-2164-12-S3-S3

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