Library of molecular associations: curating the complex molecular basis of liver diseases

Buchkremer, S.; Hendel, Jasmin; Krupp, Markus; Weinmann, Arndt; Schlamp, Kai; Maass, T; Staib, Frank; Galle, Peter R.; Teufel, Andreas

doi:10.1186/1471-2164-11-189

Cited by 14 publications

(14 citation statements)

References 22 publications

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“…A frma Z -score of >5 suggested that a gene is expressed in a particular tissue. The frma Z -score was generated to allow comparison of the expression profiles with data already present at medicalgenomics.org (16,17) and other microarray data sets processed with the frma method. Official gene symbols and National Center for Biotechnology Information (NCBI) Entrez GeneIDs were assigned to the data using the ‘hgu133plus2.db’ package.…”

Section: Methodsmentioning

confidence: 99%

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CellLineNavigator: a workbench for cancer cell line analysis

Krupp

Itzel

Maass

et al. 2012

Nucleic Acids Research

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The CellLineNavigator database, freely available at http://www.medicalgenomics.org/celllinenavigator, is a web-based workbench for large scale comparisons of a large collection of diverse cell lines. It aims to support experimental design in the fields of genomics, systems biology and translational biomedical research. Currently, this compendium holds genome wide expression profiles of 317 different cancer cell lines, categorized into 57 different pathological states and 28 individual tissues. To enlarge the scope of CellLineNavigator, the database was furthermore closely linked to commonly used bioinformatics databases and knowledge repositories. To ensure easy data access and search ability, a simple data and an intuitive querying interface were implemented. It allows the user to explore and filter gene expression, focusing on pathological or physiological conditions. For a more complex search, the advanced query interface may be used to query for (i) differentially expressed genes; (ii) pathological or physiological conditions; or (iii) gene names or functional attributes, such as Kyoto Encyclopaedia of Genes and Genomes pathway maps. These queries may also be combined. Finally, CellLineNavigator allows additional advanced analysis of differentially regulated genes by a direct link to the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources.

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Section: Methodsmentioning

confidence: 99%

“…Data on cellular component, biological process and molecular function were collected from the Gene Ontology database (26). Finally, the CellLineNavigator was cross-linked to our RNA-Seq expression profiling database on normal tissues, RNA-Seq Atlas (16), and our liver-specific Library of Molecular Associations [LoMA (17)].…”

Section: Methodsmentioning

confidence: 99%

CellLineNavigator: a workbench for cancer cell line analysis

Krupp

Itzel

Maass

et al. 2012

Nucleic Acids Research

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“…We have recently tried to address the interaction of molecular networks from gene expression data with their association to human liver diseases and generated the first comprehensive and valid database for published molecular associations to close the gap between genome wide microarray data and individual highly validated data from PubMed [61]. Currently, Library of Molecular Associations (LOMA) holds approximately 1260 manually confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC.…”

Section: Transcriptomicsmentioning

confidence: 99%

Molecular diagnosis and therapy of hepatocellular carcinoma (HCC): An emerging field for advanced technologies

Marquardt

Galle

Teufel

2012

Journal of Hepatology

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164

134

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Despite great progress in diagnosis and management of hepatocellular carcinoma (HCC), the exact biology of the tumor remains poorly understood overall limiting the patients' outcome. Detailed analysis and characterization of the molecular mechanisms and subsequently individual prediction of corresponding prognostic traits would revolutionize both diagnosis and treatment of HCC and is the key goal of modern personalized medicine. Over the recent years systematic approaches for the analysis of whole tumor genomes and transcriptomes as well as epigenomes became affordable tools in translational research. This includes simultaneous analyses of thousands of molecular targets using microarray-based technologies as well as next-generation sequencing. Although currently diagnosis and classification of hepatocellular cancers still rely on histological examination of tumor sections, these technologies show great promise to advance the current knowledge of hepatocarcinogenesis, complement diagnostic classification in a setting of microarray-aided pathology, and rationalize the individual drug selection. This review aims to summarize recent progress of system biological approaches in hepatocarcinogenesis and outline potential areas for translational application in a clinical setting. Further, we give an update about known signaling pathways active in HCC, summarize the historical application of whole genomic approaches in liver cancer and indicate ongoing experimental research utilizing novel technologies in diagnosis and treatment of this deadly disease. This will also include the discussion and characterization of new molecular and cellular targets such as Cancer Stem Cells (CSCs).

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“…The database holds confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC. The database may be searched not only by means of disease or gene names but also using pathway or gene ontology information provided by the LoMA database [24].…”

Section: Library Of Molecular Associations (Loma)mentioning

confidence: 99%

Bioinformatics and database resources in hepatology

Teufel¹

2015

Journal of Hepatology

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Lately, advances in high-throughput technologies in biomedical research have led to a dramatic increase in the accessibility of molecular insights at multiple biological levels in hepatology. Much of this information is available in publications, but an increasing number of large-scale analyses are currently being stored in databases. Scopes of these databases are very divergent and may range from large, general databases collecting information on almost every known disease, to very specialized databases covering only a specific liver disease or aspect of hepatology. Over recent years, these bioinformatics data repositories have rapidly evolved into an essential aid for molecular hepatology. However, although publicly available through the internet, many of these databases are only known to a few experts. To facilitate access to these resources, the publicly available databases supporting research on liver diseases are summarized in this review.

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Library of molecular associations: curating the complex molecular basis of liver diseases

Cited by 14 publications

References 22 publications

CellLineNavigator: a workbench for cancer cell line analysis

CellLineNavigator: a workbench for cancer cell line analysis

Molecular diagnosis and therapy of hepatocellular carcinoma (HCC): An emerging field for advanced technologies

Bioinformatics and database resources in hepatology

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