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Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

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

Cited 12 times inthomson ciCited 10 times inthomson ci
Title
Liverome: a curated database of liver cancer-related gene signatures with self-contained context information
Author
Lee, LanghoWang, KaiLi, GangXie, ZhiWang, YuliXu, JiangchunSun, ShaoxianPocalyko, DavidBhak, Jong HwaKim, ChulhongLee, Kee-HoJang, Ye JinYeom, Young IlYoo, Hyang-SookHwang, Seungwoo
Keywords
Biological insight; Biological interpretation; Candidate genes; Context information; Curation; Data coverage; Database contents; Differential expressions; Guided browsing; Hepatocellular carcinoma; Liver cancers; Molecular profiling; Prioritization; Protein expressions; Signature database; Web interface
Issue Date
2011-11
Publisher
BIOMED CENTRAL LTD
Citation
BMC GENOMICS, v.12, no.SUPPLE 3, pp. -
Abstract
Background: Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. A number of molecular profiling studies have investigated the changes in gene and protein expression that are associated with various clinicopathological characteristics of HCC and generated a wealth of scattered information, usually in the form of gene signature tables. A database of the published HCC gene signatures would be useful to liver cancer researchers seeking to retrieve existing differential expression information on a candidate gene and to make comparisons between signatures for prioritization of common genes. A challenge in constructing such database is that a direct import of the signatures as appeared in articles would lead to a loss or ambiguity of their context information that is essential for a correct biological interpretation of a gene's expression change. This challenge arises because designation of compared sample groups is most often abbreviated, ad hoc, or even missing from published signature tables. Without manual curation, the context information becomes lost, leading to uninformative database contents. Although several databases of gene signatures are available, none of them contains informative form of signatures nor shows comprehensive coverage on liver cancer. Thus we constructed Liverome, a curated database of liver cancer-related gene signatures with self-contained context information. Description: Liverome's data coverage is more than three times larger than any other signature database, consisting of 143 signatures taken from 98 HCC studies, mostly microarray and proteome, and involving 6,927 genes. The signatures were post-processed into an informative and uniform representation and annotated with an itemized summary so that all context information is unambiguously self-contained within the database. The signatures were further informatively named and meaningfully organized according to ten functional categories for guided browsing. Its web interface enables a straightforward retrieval of known differential expression information on a query gene and a comparison of signatures to prioritize common genes. The utility of Liverome-collected data is shown by case studies in which useful biological insights on HCC are produced. Conclusion: Liverome database provides a comprehensive collection of well-curated HCC gene signatures and straightforward interfaces for gene search and signature comparison as well. Liverome is available at http:// liverome.kobic.re.kr.
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DOI
10.1186/1471-2164-12-S3-S3
ISSN
1471-2164
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BME_Journal Papers
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