A. Gene Expr Patterns. Chen X, Miao Z, Divate M, Zhao Z, Cheung E. KM-express: an integrated online patient survival and gene expression analysis tool for the identification and functional characterization of prognostic markers in breast and prostate cancers. The widespread use of GENT since its launch at 2011 reflects the needs for carefully curated large-scale gene expression databases with an easy-to-use interface. 2013;6(269):pl1. The functions of the GENT2 database are listed on the right. a Forest plot of hazard ratio on the ERBB2 gene with progression-free survival. Krupp M, Itzel T, Maass T, Hildebrandt A, Galle PR, Teufel A. CellLineNavigator: a workbench for cancer cell line analysis. 2004;6(1):1–6. In the previously constructed GENT, all search and display activities were implemented using PHP and MySQL environments. However, for many researchers who do not have bioinformatics skills to fully utilize the datasets, the public datasets are of little value. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. Online ahead of print. Red indicates a boxplot of cancer samples. Google Scholar. GENT shows gene expression patterns in various tissues easily and has more than 40,000 samples for 25 normal-cancer paired tissues. For each subtype, P-value and log2 fold change are calculated. Cancer Genome Atlas N. Comprehensive molecular portraits of human breast tumours. b Statistical…, Meta-analysis. Guo Z, Zhang X, Zhu H, Zhong N, Luo X, Zhang Y, Tu F, Zhong J, Wang X, He J, Huang L. Oncol Rep. 2020 Dec 9;45(2):523-34. doi: 10.3892/or.2020.7890. Nucleic Acids Res. Hence, we adopted a meta-survival analysis into GENT2, providing reliable prognostic power estimated by synergetic effect across many independent reports. TissueScan™ Cancer and Normal Tissue cDNA Arrays qPCR gene expression results of hundreds of human samples in 2 hours TissueScan™ Cancer and Normal Tissue cDNA Arrays are developed for … Here, we integrate gene expression data from disparate sample types, disease stages and technical platforms into one coherent whole, to give a global view of the expression changes associated with the development and progression of PC from normal tissue … High mRNA expression of splice variant SYK short correlates with hepatic disease progression in chemonaive lymph node negative colon cancer patients. Lastly, the TiGER database contains EST data around several tissues. COVID-19 is an emerging, rapidly evolving situation. These databases have the benefit of comparing information between two high-throughput platforms. In the near future, we plan to update GENT2 to enable multiple gene search and add RNA-sequencing data as well as microarrays. Springer Nature. Next, the upper layer is a tab that allows users to select each window for different analyses. GENT2 is freely available at http://gent2.appex.kr. A public database, SAGEmap, was created as a component of the Cancer Genome Anatomy Project to provide a central location for depositing, retrieving, and analyzing human gene expression data. We used the same MAS5 algorithm used in the original GENT, as it is a single-array algorithm, which allows the comparison of multiple independent datasets [1]. doi: 10.1093/nar/gkx907. -, Coebergh van den Braak RRJ, Sieuwerts AM, Kandimalla R, Lalmahomed ZS, Bril SI, van Galen A, Smid M, Biermann K, van Krieken J, Kloosterman WP, et al. Second, with increasing importance of tumor subtypes, GENT2 provides an option to study the differential expression and its prognostic significance based on tumor subtypes. 2004;20(3):307–15. We collected data from the GEO public repository using only two platforms, U133Plus2 (GPL570) and U133A (GPL96). Statistical tests are also performed for each subtype (Fig. Wang Z, He Y, Deng W, Lang L, Yang H, Jin B, Kolhe R, Ding HF, Zhang J, Hai T, et al. Compared to normal, ERBB2 was overexpressed in a few tumors including from bone, breast, and ovary. eCollection 2020 Dec. Nie Y, Zhao Z, Chen M, Ma F, Fan Y, Kang Y, Kang B, Wang C. Oncol Lett. Bioinformatics. PLoS One. Lee J, Choi C. Oncopression: gene expression compendium for cancer with matched normal tissues. First, Oncopression, CellLineNavigator, and MERAV are databases that can investigate gene profiling around the collected microarray datasets for various cancer types. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. As expected, the HER2 group has the highest value on average, and the TNBC group has the lowest value. TE is the estimated treatment effect, seTE is the standard error of the treatment estimate, and HR indicates the hazard ratio average. Nucleic Acids Res. By using GWT framework, user-friendly and flexible web interfaces were equipped in the GENT2, and real-time interactions between web-client and server systems through GWT RPC method were also available. Thus, we undertook the present study with the goal of expanding and consolidating the expression profile of p63 in human normal and tumor Received 8/6/01; revised 10/2… Five tumor types that show >25% expression percentile within each analysis set in both genes … Gene. Here, GENT2 is provided as an updated version of GENT with more samples and newer functionalities. GENT2 contains more than 44,000 (U133Plus2; 887 datasets) and 23,000 (U133A; 358 datasets) samples (Table 1, Additional file 1: Table S1, Additional file 2: Table S2). -, Wang Z, He Y, Deng W, Lang L, Yang H, Jin B, Kolhe R, Ding HF, Zhang J, Hai T, et al. Endoplasmic reticulum stress activates SRC, relocating chaperones to the cell surface where GRP78/CD109 blocks TGF-beta signaling. The full contents of the supplement are available online at https://bmcmedgenomics.biomedcentral.com/articles/supplements/volume-12-supplement-5. Third, whenever available, GENT2 provides prognostic information of a gene of interest. USA.gov. 2017;77(1):74–85. We collected data from the GEO public repository using only two platforms, U133Plus2 (GPL570) and U133A (GPL96). These samples are called "solid tissue normals" and are taken from normal tissues near the tumor. 2008 Feb;8(3):171-80. doi: 10.1016/j.gep.2007.10.011. Data on p63 expression are limited mainly to Northern blots, thus lacking microanatomical details. GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. The GENT2 main page consists of three layers for user convenience. Results: Epub 2020 Dec 10. Nucleic Acids Res. 1b, compared with normal tissues, most tumor types show significantly higher expression of AURKA, except for pancreatic adenocarcinoma (PAAD), PCPG, skin cutaneous melanoma (SKCM), and thymoma (THYM). However, GENT2 has many useful features such as subtype analysis and meta-survival analysis, which are not available in other databases. et al. Second, with increasing importance of tumor subtypes, GENT2 provides an option to study the differential expression and its prognostic significance based on tumor subtypes. An Update. https://doi.org/10.1186/s12920-019-0514-7, DOI: https://doi.org/10.1186/s12920-019-0514-7. Searching the MERAV database for the expression of these metabolic enzymes both in normal tissues and in cancer cell lines shows that the expression levels of all three genes are significantly elevated in cancer cells (Figure 2C and D). Expression Atlas update: from tissues to single cells Nucleic Acids Research, 30 October 2019. We thank Drs Sung-Min Park and Jong-Hwan Kim for their helpful comments on the GENT2 website and the manuscript. MENT: methylation and expression database of normal and tumor tissues. The expression ratios of each gene in 6 tissues … Thus, we applied recent informatics technologies including GWT and Lucene into the GENT2. Proc Natl Acad Sci U S A. Manage cookies/Do not sell my data we use in the preference centre. For each tissue, P-value and log2 fold change are calculated, and NA at the ‘P-value’ column means that there is only one sample of normal tissue. Article  Cite this article. Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. a A boxplot across 72 paired tissues in GPL570 only. For instance, Oncopression [12], CellLineNavigator [13], MERAV [14], Oncomine [15], cBioPortal [16], RNA Seq Atlas [17], KM-Express [18], BioXpress [19], TiGER [20], and so on (Table 4). Would you like email updates of new search results? Xena offers two sources of normal tissue: TCGA's solid tisue normal samples from individuals with cancer, and GTEX normal tissue from individuals who do not have cancer. By comparing gene expression profiles of colorectal cancer and adjacent normal tissues, 1-class capabilities in SAM software filtered out 3,680 differentially expressed genes (P≤0.05), of which 2,043 genes were upregulated and 1,637 genes were downregulated in cancer tissues compared with normal tissues. As shown in Fig. We suggest that comparing multiple datasets researchers can obtain more reliable prognostic information. Overview of the GENT2 database system. 2018;2018. To construct the GENT2 system, gene expression data is downloaded from the NCBI GEO database generated by two microarray platforms (Affymetrix U133A or U133Plus2). PubMed  Park, SJ., Yoon, BH., Kim, SK. In particular, the ERBB2 gene has a highly distinct expression pattern with relatively all significant differences in each group. Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea, Seung-Jin Park, Byoung-Ha Yoon & Seon-Young Kim, Department of Bioscience, University of Science and Technology (UST), Daejeon, 34113, Korea, Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Korea, You can also search for this author in Second, GENT2 provides gene expression information on 72 paired tissues compared to 57 tissues of GENT. Database. Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu TJ, Yan C, Zhang H, Mazumder R. BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. Gautier L, Cope L, Bolstad BM, Irizarry RA. b Summary and statistics test of a. 2012;490(7418):61–70. a Box and dot-plot of each subtype. For example, the GSE9195 dataset is an experiment to identify the effect of tamoxifen in estrogen receptor positive (ER+) breast cancer [10], while the GSE16446 dataset is also an experiment to uncover the effect of anthracycline in estrogen receptor negative (ER-) breast cancer [11]. Get the latest public health information from CDC: https://www.coronavirus.gov, Get the latest research information from NIH: https://www.nih.gov/coronavirus, Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. In samples from patients with 27 out of 33 tumor … doi: 10.4137/CIN.S7226. GENT: gene expression database of normal and tumor tissues. Cancer Informat. Third, whenever available, GENT2 provides prognostic information of a gene of interest. Then, the data were stratified into cancer and normal samples across 72 tissues. With GENT2, we continue to provide the core functions of GENT; however, with increasing public datasets, we updated and expanded the GENT database in terms of datasets and novel useful functions. In conclusion, with these significant improvements, GENT2 will continue to be a useful tool to a wide range of researchers. (PNG 16 kb), Table S2. a Forest plot of hazard ratio on the ERBB2 gene with progression-free…, User Interface. Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, et al. The GENT2 main page consists of three layers for user convenience.…, NLM Coebergh van den Braak RRJ, Sieuwerts AM, Kandimalla R, Lalmahomed ZS, Bril SI, van Galen A, Smid M, Biermann K, van Krieken J, Kloosterman WP, et al. Major improvements of GENT2 over GENT are the following. The authors declare that they have no competing interests. Clipboard, Search History, and several other advanced features are temporarily unavailable. Meta-analysis. Third, GENT provides intuitive graphics as well as raw gene expression values to users, so users can utilize the information in convenient ways. Cancer Inform.  |  The explosion of publicly available datasets in the cancer genomics field has provided cancer researchers invaluable resources. Cancer Informat. 2018;46(D1):D1128–36. Fourth, considering the importance of tumor subtypes, GENT2 provides results of various cancer subtype profiling analysis (e.g., stage or grade with various molecular subtypes), Fifth, it provides results of prognostic value estimation using Kaplan-Meier plots. 2.7.0) and GWT extended (GXT, ver. -, Tsai YL, Ha DP, Zhao H, Carlos AJ, Wei S, Pun TK, Wu K, Zandi E, Kelly K, Lee AS. CAS  Cancer subtype profiling; Large scale microarray web-database; Meta-survival analysis; Survival analysis; Tissue and cell line wide gene expression profiling. Finally, the center layer is a main window for displaying analysis results such as plots and tables. Notably, AURKA expression is reduced in tumor tissues versus normal tissues in the THCA dataset. To our satisfaction, since its launch at 2011, GENT has been widely used by researchers across the world, with over 1600 visitors per month on average, and the method has been cited more than 100 times in research work [2,3,4,5,6]. advantage when searching for genes over-expressed in only a subset of patients. BMC Genomics. Blue indicates a boxplot of normal samples. cancer (12, 13). 2013;41(Database issue):D942–8. Normal … Baek SJ, Yang S, Kang TW, Park SM, Kim YS, Kim SY. This article has been published as part of BMC Medical Genomics Volume 12 Supplement 5, 2019: Selected articles from the 8th Translational Bioinformatics Conference: Medical Genomics. Many databases have been developed that show gene expression of cancer samples. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. Displays study name as well as GSE, GPL, and probe information. Table S1. Sapio L, Salzillo A, Ragone A, Illiano M, Spina A, Naviglio S. Cancers (Basel). The SAGE Genie database has been developed to allow in silico analysis of gene expression and comparison of transcript levels in a large number of normal and diseased tissues [ 23 ]. Upon exponentially increased gene expression data that are publicly available, there has been a great need to upgrade system architecture of the GENT to efficiently handle those huge data sets. 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