GENT2: An Updated Gene Expression Database for Normal and Tumor Tissues

Introduction

Gene Expression database of Normal and Tumor tissues 2 (GENT2) is an updated version of GENT, which has provided a user-friendly search platform for gene expression patterns across different normal and tumor tissues compiled from public gene expression data sets. We refactored GENT2 with recent technologies such as Apache Lucene indexing for fast search and Google Web Toolkit (GWT) framework for a user-friendly web interface. Now, GENT2 contains more than 68,000 samples and has several new useful functions. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. Second, with increasing importance of tumor subtypes, GENT2 provides an option to study the differential expression and its prognostic significance based on tumor subtypes. Third, whenever available, GENT2 provides prognostic information of a gene of interest. Fourth, GENT2 provides a meta-analysis of survival information to provide users more reliable prognostic value of a gene of interest. In conclusion, with these significant improvements, GENT2 will continue to be a useful tool to a wide range of researchers. GENT2 is freely available at http://gent2.appex.kr.

Keywords: Cancer subtype profiling; Large scale microarray web-database; Meta-survival analysis; Survival analysis; Tissue and cell line wide gene expression profiling.

Please cite your use of GENT2 in your publication:

Park SJ, Yoon BH, Kim SK*, Kim SY*. GENT2: an updated gene expression database for normal and tumor tissues. BMC Med Genomics. 2019 Jul 11;12(Suppl 5):101. doi: 10.1186/s12920-019-0514-7.

Resources:

You can download a SQL dump file that contains all resources of the GENT2 including gene expression, subtype, and survival data:

GENT2_dump.sql.gz

You can import this file into MySQL DBMS for re-use. The dump file consists of a number of tables as followings:

Tables in GENT2	Remarks
GeneProfile_U133A_GeneSymbol	Gene expression data on Affymetrix U133A platform processed by gene symbol
GeneProfile_U133A_Probe	Gene expression data on Affymetrix U133A platform processed by probe ID
GeneProfile_U133Plus2_GeneSymbol	Gene expression data on Affymetrix U133Plus2 platform processed by gene symbol
GeneProfile_U133Plus2_Probe	Gene expression data on Affymetrix U133Plus2 platform processed by probe ID
MetaAnalysis_Survival	The survival analysis results estimated by Cox proportional hazard model
Subtype_Data	Gene expression data with molecular or pathological subtypes, follow-up time, and censor data
Subtype_Meta	Meta-data for subtype profiling