CellMinerHCC: a microarray‐based expression database for hepatocellular carcinoma cell lines

Therapeutic options for hepatocellular carcinoma (HCC) still remain limited. Development of gene targeted therapies is a promising option. A better understanding of the underlying molecular biology is gained in in vitro experiments. However, even with targeted manipulation of gene expression varying treatment responses were observed in diverse HCC cell lines. Therefore, information on gene expression profiles of various HCC cell lines may be crucial to experimental designs. To generate a publicly available database containing microarray expression profiles of diverse HCC cell lines.

[1]  Wei He,et al.  Distribution of metalloproteins in hepatocellular carcinoma and surrounding tissues. , 2007, Hepato-gastroenterology.

[2]  Jian-min Wu,et al.  Evidence of aberrant lipid metabolism in hepatitis C and hepatocellular carcinoma. , 2010, HPB : the official journal of the International Hepato Pancreato Biliary Association.

[3]  Jon W. Huss,et al.  BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources , 2009, Genome Biology.

[4]  J F Hocquette,et al.  Where are we in genomics? , 2005, Journal of physiology and pharmacology : an official journal of the Polish Physiological Society.

[5]  J. Blake,et al.  Creating the Gene Ontology Resource : Design and Implementation The Gene Ontology Consortium 2 , 2001 .

[6]  P. Galle,et al.  Microarray-Based Gene Expression Analysis of Hepatocellular Carcinoma , 2010, Current genomics.

[7]  Giuseppe Palmieri,et al.  HCV-related hepatocellular carcinoma: From chronic inflammation to cancer. , 2010, Clinical immunology.

[8]  S. Kwon,et al.  Association of TP53 mutations with stem cell-like gene expression and survival of patients with hepatocellular carcinoma. , 2011, Gastroenterology.

[9]  V. Kähäri,et al.  Matrix metalloproteinases in cancer: Prognostic markers and therapeutic targets , 2002, International journal of cancer.

[10]  Ugur Sahin,et al.  RNA-Seq Atlas - a reference database for gene expression profiling in normal tissue by next-generation sequencing , 2012, Bioinform..

[11]  Elspeth A. Bruford,et al.  Genenames.org: the HGNC resources in 2015 , 2014, Nucleic Acids Res..

[12]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[13]  M. Ronaghi,et al.  Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data , 2010, PloS one.

[14]  I. Ng,et al.  Liver cancer stem cells: implications for a new therapeutic target , 2009, Liver international : official journal of the International Association for the Study of the Liver.

[15]  Michael J. Lush,et al.  genenames.org: the HGNC resources in 2011 , 2010, Nucleic Acids Res..

[16]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[17]  Ewan Birney,et al.  Genome browsing with Ensembl: a practical overview. , 2007, Briefings in functional genomics & proteomics.

[18]  Harald Binder,et al.  Genetic signatures shared in embryonic liver development and liver cancer define prognostically relevant subgroups in HCC , 2012, Molecular Cancer.

[19]  V. Mazzaferro,et al.  Genome‐wide molecular profiles of HCV‐induced dysplasia and hepatocellular carcinoma , 2007, Hepatology.

[20]  S. Thorgeirsson,et al.  A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells , 2006, Nature Medicine.

[21]  V. McKusick.  Mendelian Inheritance in Man and Its Online Version, OMIM , 2007, The American Journal of Human Genetics.

[22]  S. Thorgeirsson,et al.  Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling , 2004, Hepatology.

[23]  Maria Gazouli,et al.  Stem cells in colon cancer. A new era in cancer theory begins , 2010, International Journal of Colorectal Disease.

[24]  P. Galle,et al.  Collecting evidence for a stem cell hypothesis in HCC , 2010, Gut.

[25]  Xin Wei Wang,et al.  Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment. , 2006, Cancer cell.

[26]  Thorsten Maass,et al.  Library of molecular associations: curating the complex molecular basis of liver diseases , 2010, BMC Genomics.

[27]  S. Thorgeirsson,et al.  Functional and genomic implications of global gene expression profiles in cell lines from human hepatocellular cancer , 2002, Hepatology.

[28]  S. Friedman,et al.  Obesity, inflammatory signaling, and hepatocellular carcinoma-an enlarging link. , 2010, Cancer cell.

[29]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[30]  M. Todaro,et al.  Immunotherapy targeting colon cancer stem cells. , 2011, Immunotherapy.

[31]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[32]  P. Galle,et al.  IFN-alpha-induced apoptosis in hepatocellular carcinoma involves promyelocytic leukemia protein and TRAIL independently of p53. , 2009, Cancer research.

[33]  Xuegong Zhang,et al.  Comparison of gene expression in hepatocellular carcinoma, liver development, and liver regeneration , 2010, Molecular Genetics and Genomics.

[34]  M. Kanehisa,et al.  Using the KEGG Database Resource , 2005, Current protocols in bioinformatics.

[35]  Tae-Wook Kang,et al.  GENT: Gene Expression Database of Normal and Tumor Tissues , 2011, Cancer informatics.

[36]  A. Schetter,et al.  Inflammation and cancer: interweaving microRNA, free radical, cytokine and p53 pathways. , 2010, Carcinogenesis.