Of the 10,687 cross-mapped common genes analyzed on the Expression Array System, 6,893 genes are present in both the normal and tumor samples and 862 genes have > 2 … Baek SJ, Yang S, Kang TW, Park SM, Kim YS, Kim SY. Terms and Conditions, 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… National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error, Overview of the GENT2 database system. Results: Inhibition of PCSK9 potentiates immune checkpoint therapy for cancer. Solid tissue normal samples from TCGA are typically limited in number but some cancer … PubMed  Compared with MySQL system, Lucene indexing in the GENT2 showed a better performance accessing faster than approximately 10 times. We collected data from the NCBI GEO public database and processed them with the MAS5 algorithm using the affy package in Bioconductor [7]. The system architecture of GENT2 is illustrated in Additional file 3: Figure S1. These samples are called "solid tissue normals" and are taken from normal tissues near the tumor. Nucleic Acids Res. BMC Genomics. 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. The full contents of the supplement are available online at https://bmcmedgenomics.biomedcentral.com/articles/supplements/volume-12-supplement-5. We collected data from the GEO public repository using only two platforms, U133Plus2 (GPL570) and U133A (GPL96). 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. Cancer Informat. 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. Tissue-wide gene expression pattern of ERBB2 gene across 72 paired tissues and statistical tests. First, Oncopression, CellLineNavigator, and MERAV are databases that can investigate gene profiling around the collected microarray datasets for various cancer types. Validation of CSN1S1 transcriptional expression, promoter methylation, and prognostic power in breast cancer using independent datasets. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. First, GENT2 contains more than 68,000 samples compared to 34,000 samples in GENT. 1). 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. GENT: gene expression database of normal and tumor tissues. PLoS One. Feng C, Araki M, Kunimoto R, Tamon A, Makiguchi H, Niijima S, Tsujimoto G, Okuno Y. BMC Genomics. Google Scholar. Use our TissueScan qPCR arrays to reveal gene expression profiles across disease stages, while also assessing expression … Many databases have been developed that show gene expression of cancer samples. Liu X, Yu X, Zack DJ, Zhu H, Qian J. TiGER: a database for tissue-specific gene expression and regulation. The authors declare that they have no competing interests. The explosion of publicly available datasets in the cancer genomics field has provided cancer researchers invaluable resources. 2012;28(8):1184–5. 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. a Box and dot-plot of each subtype. The number of different tissues increased from 57 to 72, and new functions such as subtype profiling, various statistical tests, and meta-survival analysis were added. To identify the genes and molecules associated with poor prognosis of early-onset breast cancer, we examined gene expression profiles from paired breast normal/ tumor tissues, and coupled with Gene Ontology and public data base … Correspondence to -. BMC Med Genomics 12, 101 (2019). User Interface. statement and doi: 10.1093/nar/gkx907. The expression ratios of each gene in 6 tissues … 2017;12(9):e0185607. See this image and copyright information in PMC. https://doi.org/10.1186/s12920-019-0514-7, DOI: https://doi.org/10.1186/s12920-019-0514-7. Compared to normal, ERBB2 was overexpressed in a few tumors including from bone, breast, and ovary. Each database has its own unique advantages. Atf3 deficiency promotes genome instability and spontaneous tumorigenesis in mice. Belgium, Brussels. Next, we classified the data into cancer and normal tissue. eCollection 2020 Dec. Nie Y, Zhao Z, Chen M, Ma F, Fan Y, Kang Y, Kang B, Wang C. Oncol Lett. GENT2 is freely available online at http://gent2.appex.kr. Gene. © 2021 BioMed Central Ltd unless otherwise stated. Background: Google Scholar. Finally, the center layer is a main window for displaying analysis results such as plots and tables. Example: MYC expression. In many respects, they are very similar to GENT2 database. 2018;115(18):E4245–54. We recently provided a large-scale cancer gene expression database named GENT (Gene Expression database of Normal and Tumor tissues) by collecting and processing more than 34,000 … Enormous amounts of publicly available gene expression datasets have accumulated since GENT was first published in 2011, and the need was recognized to upgrade the GENT system both quantitatively and qualitatively. Hi all I want to download those samples from TCGA website, which have both gene expression and miRNA expression data from both tumor and normal tissues ( matched normal and tumor samples) . Springer Nature. Nature. The explosion of publicly available omics datasets including gene expression microarray and next-generation sequencing has provided valuable resources for researchers. Online ahead of print. Krupp M, Itzel T, Maass T, Hildebrandt A, Galle PR, Teufel A. CellLineNavigator: a workbench for cancer cell line analysis. Table S1. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. This … This result suggests that the prognostic value of ERBB2 can be different according to different contexts. All interactions in the server layer were implemented by R, RCaller, Apache Lucene software. U133Plus2 data description in GENT2. b Summary and statistics test of a. The GENT2 infrastructure consists of web browser and server layers. Cancer Res. U133A data description in GENT2.  |  2006 Dec 1;22(23):2898-904. doi: 10.1093/bioinformatics/btl500. All statistical tests provided from the GENT2, such as two-sample t-test, Kaplan-Meier with log-rank test, and meta-survival analysis with Cox proportional hazard modes, were implemented using R (ver. Seon-Kyu Kim or Seon-Young Kim. 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. The top three tissues of each platform are as follows: blood, brain and breast for U133Plus2 and blood, bone marrow and brain for U133A. When a user puts a gene symbol in the ‘Search Gene profile’ page, GENT2 performs tissue-wide expression profiling and statistical testing quickly (less than 5 s) on two Affymetrix platforms, simultaneously. Nucleic Acids Res. 2012;490(7418):61–70. An Update. Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. This is the data list for the U133Plus2 platform in the GENT2 database. User Interface. The GENT2 database provides the following five functions: 1) a landscape of gene expression profile across 72 normal and tumor tissues, 2) cancer subtype profiling, 3) statistical significance of gene expression difference between normal and tumor samples, 4) a prognostic value of gene expression, and 5) meta-survival analysis (Fig. Wang Z, He Y, Deng W, Lang L, Yang H, Jin B, Kolhe R, Ding HF, Zhang J, Hai T, et al. A graphical user interface (GUI) was implemented using Google Web Toolkit (GWT) and GWT extended (GXT) frameworks. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. Overview of the GENT2 database system. 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. Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, et al. Confirming the prognostic relevance of a gene is important for its application in the clinical field. 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 … 2017;77(1):74–85. Multifactorial approach to predicting resistance to anthracyclines. Liu X, Bao X, Hu M, Chang H, Jiao M, Cheng J, Xie L, Huang Q, Li F, Li CY. We collected data from the GEO public repository using only two platforms, U133Plus2 (GPL570) and U133A (GPL96).