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

Abstract

BackgroundHepatocellular 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.DescriptionLiverome’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.ConclusionLiverome 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.

Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH

“…The data suggest reprogramming of one-carbon metabolism in HCC. This is consistent with the Liverome study reporting that downregulation of MTHFD1 is prevalent in proliferative and poorly differentiated HCCs 38 .…”

Identifying microRNA panels specifically associated with hepatocellular carcinoma and its different etiologies

“…Among target genes, 130 genes have been associated with HCC in at least one previous report by comparing with Liverome database (http://liverome.kobic.re.kr/). [21] Upon further evaluation for enriched biological function, we identified several important biologic pathways, including transforming growth factor beta (TGFβ) receptor signaling pathway, endocytosis, signaling by epidermal growth factor receptor, signaling by nerve growth factor (NGF), NGF signaling via tropomyosin receptor kinase A from the plasma membrane, BMAL1: CLOCK/NPAS2 activates circadian expression and adherens junction [Supplementary Table 7], which confirmed the potential biological role of HCC specific miRNAs involved in tumorigenesis.…”

Glypican‐3: a marker and a therapeutic target in hepatocellular carcinoma

“…HCCs are highly heterogeneous, and it is unlikely that a single marker will be found that is expressed in 100% of patients . Di Tommaso et al .…”

“…HCCs are highly heterogeneous, and it is unlikely that a single marker will be found that is expressed in 100% of patients [30]. Di Tommaso et al have shown that the simultaneous use of GPC3, heat shock protein 70 (HSP70) and glutamine synthetase (GS) immunostaining could significantly increase sensitivity without reducing specificity of the GPC3-only based diagnosis of HCC [31,32].…”