Differentially expressed genes in colorectal cancer and adjacent cancer tissues. In conclusion, with these significant improvements, GENT2 will continue to be a useful tool to a wide range of researchers. 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]. -, Wang Z, He Y, Deng W, Lang L, Yang H, Jin B, Kolhe R, Ding HF, Zhang J, Hai T, et al. 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. 2a, for example, we illustrate the tissue-wide gene expression profile of an oncogene, ERBB2. Sapio L, Salzillo A, Ragone A, Illiano M, Spina A, Naviglio S. Cancers (Basel). Additionally, subtype analysis and meta-analysis data in GENT2 are displayed in Tables 2 and 3, respectively. CAS A. Second, with increasing importance of tumor subtypes, GENT2 provides an option to study the differential expression and its prognostic significance based on tumor subtypes. This is the data list for the U133A platform in the GENT2 database. b Summary and statistics test of a. User Interface. Fourth, GENT2 provides a meta-analysis of survival information to provide users more reliable prognostic value of a gene of interest. -. For Blood, more than 10 K samples are stored. as well as boxplot summaries for user convenience. Epub 2020 Dec 10. 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. a Box and dot-plot of each subtype. Baek SJ, Yang S, Kang TW, Park SM, Kim YS, Kim SY. Lastly, the TiGER database contains EST data around several tissues. 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. Cancer Genome Atlas N. Comprehensive molecular portraits of human breast tumours. We thank Drs Sung-Min Park and Jong-Hwan Kim for their helpful comments on the GENT2 website and the manuscript. We collected data from the GEO public repository using only two platforms, U133Plus2 (GPL570) and U133A (GPL96). expressed genes (> 2-fold changes between tumor and normal samples) are shown in red. We collected data from the NCBI GEO public database and processed them with the MAS5 algorithm using the affy package in Bioconductor . Proc Natl Acad Sci U S A. 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 … First, the left layer is used to select three functions and can be hidden by clicking the arrow button. Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. 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. Second, with increasing importance of tumor subtypes, GENT2 provides an option to study the differential expression and its prognostic significance based on tumor subtypes. 2013;6(269):pl1. Statistical tests are also performed for each subtype (Fig. Nicolas Rosewick ♦ 9.3k wrote: Hi, SInce TCGA data are now on NCI website how can I download gene expression data (FPKM) for breast cancer and associated normal tissue. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. https://doi.org/10.1186/s12920-019-0514-7, DOI: https://doi.org/10.1186/s12920-019-0514-7. The full contents of the supplement are available online at https://bmcmedgenomics.biomedcentral.com/articles/supplements/volume-12-supplement-5. ‘Search Gene profile’ provides two boxplots of gene expression from the Affymetrix U133Plus2 and the Affymetrix U133A platform, allowing users to compare both results. GENT2 system architecture. MERAV: a tool for comparing gene expression across human tissues and cell types. | Description: GENT (Gene Expression database of Normal and Tumor tissues) is a web-accessible database that provides gene expression patterns across diverse human cancer and normal 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. 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… Article Please enable it to take advantage of the complete set of features! 2011;29(12):1578–86. ERBB2 is a representative oncogene activated in breast cancer . (A) Tumor types ranked by expression percentile in each gene. Shaul YD, Yuan B, Thiru P, Nutter-Upham A, McCallum S, Lanzkron C, Bell GW, Sabatini DM. Atf3 deficiency promotes genome instability and spontaneous tumorigenesis in mice. 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. Tissue-wide gene expression pattern of ERBB2 gene across 72 paired tissues and statistical tests. Clipboard, Search History, and several other advanced features are temporarily unavailable. Data exchange between a web browser and the GENT2 server is controlled by a GWT remote procedure call. The GENT2 infrastructure consists of web browser and server layers. 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. Nucleic Acids Res. 2018;115(18):E4245–54. PubMed There are two main sources of normal expression data in Xena. Tissue-wide gene expression pattern of ERBB2 gene across 72 paired tissues and statistical tests. The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data Bioinformatics , … We collected data from the GEO public repository using only two platforms, U133Plus2 (GPL570) and U133A (GPL96). Publication costs are funded by grants from the National Research Foundation of Korea (NRF-2017MBA9B5060884 and NRF-2014M3C9A3068554), and grant from KRIBB Research Initiative Program. BMC Bioinformatics. However, for many researchers who do not have bioinformatics skills to fully utilize the datasets, the public datasets are of little value. HER2 and EGFR overexpression support metastatic progression of prostate cancer to bone. Meta-analysis. TELO2 induced progression of colorectal cancer by binding with RICTOR through mTORC2. PLoS One. 2018;2018. SJP, SKK, and SYK wrote the manuscript, and all authors read and approved the manuscript. Bioinformatics. Red indicates a boxplot of cancer samples. Inhibition of PCSK9 potentiates immune checkpoint therapy for cancer. Online ahead of print. The authors declare that they have no competing interests. c Kaplan-Meier plots by subtypes and median cut-off. Question: Download TCGA cancer and normal tissue gene expression data from GDC . 2004;20(3):307–15. Ouyang M, Garnett AT, Han TM, Hama K, Lee A, Deng Y, Lee N, Liu HY, Amacher SL, Farber SA, Ho SY. 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) . HHS 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 … In our opinion, a few strengths have contributed to the success of GENT. Tsai YL, Ha DP, Zhao H, Carlos AJ, Wei S, Pun TK, Wu K, Zandi E, Kelly K, Lee AS. In GENT2, we added the following two novel functions: subtype profiling and survival analysis. 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. Normal … Overview of the GENT2 database system. doi: 10.1371/journal.pone.0185607. As shown in Fig. 2018;46(D1):D1128–D1136. Hence, we adopted a meta-survival analysis into GENT2, providing reliable prognostic power estimated by synergetic effect across many independent reports. 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. a A boxplot across 72 paired tissues in GPL570 only. COVID-19 is an emerging, rapidly evolving situation. If a case only has the tumor … 2018;46(D1):D1128–36. Terms and Conditions, Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 2012;490(7418):61–70. We also adopted recent technologies such as such the GWT web framework and a Lucene indexing machine to provide more user-friendly web experiences. 4.5 years ago by. User Interface. The authors declare that they have no competing interests. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. doi: 10.1093/nar/gkx907. Description:GENT (Gene Expression database of Normal and Tumor tissues) is a web-accessible database that provides … We suggest that comparing multiple datasets researchers can obtain more reliable prognostic information. 2013 Apr 10;518(1):194-200. doi: 10.1016/j.gene.2012.11.032. Article Oncogene. Third, GENT provides intuitive graphics as well as raw gene expression values to users, so users can utilize the information in convenient ways. NIH Lee J, Choi C. Oncopression: gene expression compendium for cancer with matched normal tissues. ONCOMINE: a cancer microarray database and integrated data-mining platform. Major improvements of GENT2 over GENT are the following. 2020 Oct 28;12(11):3166. doi: 10.3390/cancers12113166. Endoplasmic reticulum stress activates SRC, relocating chaperones to the cell surface where GRP78/CD109 blocks TGF-beta signaling. A graphical user interface (GUI) was implemented using Google Web Toolkit (GWT) and GWT extended (GXT) frameworks. Blue indicates genes that are changed < 2-fold. | Springer Nature. TE is the estimated treatment effect, seTE is the standard error of the treatment estimate, and HR indicates the hazard ratio average. Epub 2006 Oct 10. GENT2 is freely available at http://gent2.appex.kr. Endoplasmic reticulum stress activates SRC, relocating chaperones to the cell surface where GRP78/CD109 blocks TGF-beta signaling. 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). © 2021 BioMed Central Ltd unless otherwise stated. Privacy 2021 Feb;21(2):107. doi: 10.3892/ol.2020.12368. This … Desmedt C, Di Leo A, de Azambuja E, Larsimont D, Haibe-Kains B, Selleslags J, Delaloge S, Duhem C, Kains JP, Carly B, et al. In the near future, we plan to update GENT2 to enable multiple gene search and add RNA-sequencing data as well as microarrays. 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. Epub 2011 May 9. 3a. The explosion of publicly available omics datasets including gene expression microarray and next-generation sequencing has provided valuable resources for researchers. They show that MYC gene expression … Belgium, Brussels. This result suggests that the prognostic value of ERBB2 can be different according to different contexts. The GENT2 main page consists of three layers for user convenience. Subtype and survival analysis. 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/. Second, the large amounts of samples (~ 34,000) generated using the same platform with consistent data processing makes the database reliable by removing or reducing many biases (i.e., different batches, laboratories, ethnicities, etc.) Results: Cancer Informat. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. 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 . Many databases have been developed that show gene expression of cancer samples. Although the ERBB2 gene showed distinct expression patterns, the log-rank test p-value for each group was found to be insignificant, suggesting that expression difference is irrelevant of prognostic difference. In many respects, they are very similar to GENT2 database. Finally, survival analysis is performed for each subtype (Fig. Table S1. Atf3 deficiency promotes genome instability and spontaneous tumorigenesis in mice. All interactions in the server layer were implemented by R, RCaller, Apache Lucene software. To assess the ability of the barcode algorithm to find undiscovered tissue subsets, we used data from three breast cancer studies that did not include normal breast tissue samples, but did include patient survival data 14–16.The distance to all tissue barcodes was obtained and 499 of the 500 samples were classified as breast tumor (1 as bladder cancer). Example: MYC expression. Nucleic Acids Res. Keywords: First, it is very simple to use. There are no cell-line data from U133A platform around all tissues. Blue indicates a boxplot of normal samples. 1). As RNA-seq has become the de facto standard method for exploring gene expression, we plan to add gene expression datasets produced by RNA-seq in the future version of GENT. Primarily focusing on gene expression data of the normal tissues of the head and neck, the cancer genome atlas (TCGA) database was used to identify groups of genes that were expressed synergistically with the COP9 genes… With those improvements in both data volume and novel functions, GENT2 will continue to be a useful tool to help researchers in the field of cancer genomics. Currently, a subtype analysis function provides information on 46 subtypes of 19 tissue types with over 13,000 samples. Each database has its own unique advantages. Notably, AURKA expression is reduced in tumor tissues versus normal tissues in the THCA dataset. With these significant improvements, GENT2 is suggested as a versatile tool to assess the biological and prognostic relevance of a specific gene in various cancers. -, Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. GENT2 is freely available at http://gent2.appex.kr . BMC Genomics. Background: The first is normal samples from TCGA itself. It is becoming easier to profile gene expression at system levels, and vast amount of such profile results continue to be deposited in public database such as Gene Expression Omnibus (GEO) (Barrett et al., 2013), ArrayExpress (AE) (Parkinson et al., 2007) and International Cancer Genome Consortium (ICGC) (Zhang et al., 2011).Besides the data … In Fig. 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. doi: 10.4137/CIN.S7226. Krupp M, Itzel T, Maass T, Hildebrandt A, Galle PR, Teufel A. CellLineNavigator: a workbench for cancer cell line analysis. For instance, the expression pattern for the molecular subtype of the ERBB2 gene in breast cancer tissue is shown in Fig. b Statistical test based on each subtype. If a user selects a tissue and a specific subtype, GENT2 provides the expression profiling of subtypes of the selected tissue. Gene. (PNG 16 kb), Figure S1. The ratios of each gene to control Actin beta were measured using total RNAs from 3 normal tissues and 3 tumor tissues, which were also used for gene expression profiling. In particular, Blood, Breast, Colon, Kidney, Skin, and Bladder tissues contain all kinds of data. a Forest plot of hazard ratio on the ERBB2 gene with progression-free survival. Fixed and random effects are shown. GENT2 is freely available online at http://gent2.appex.kr. 2011;10:149–157. A larger number of samples were added to the original GENT, and over 380 datasets were added for the U133Plus2 platform. Epub 2012 Dec 7. 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. Many studies have reported incongruent prognostic characteristics of a gene, thus there is a great need to further evaluate the prognostic potential of a gene by combining multiple information across many studies. Comparing information between two high-throughput platforms a tab that allows users to select three functions and can hidden! Been developed that show gene expression information on 72 paired tissues in GPL570 only variant. Data list for the U133A platform around all tissues than approximately 10 times protein data covers 15320 (... 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