The expression ratios of each gene in 6 tissues … HER2 and EGFR overexpression support metastatic progression of prostate cancer to bone. GENT2 is freely available at http://gent2.appex.kr. Expression Atlas update: from tissues to single cells Nucleic Acids Research, 30 October 2019. 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]. 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) . High mRNA expression of splice variant SYK short correlates with hepatic disease progression in chemonaive lymph node negative colon cancer patients. Blue indicates a boxplot of normal samples. A user inputs a gene symbol of interest and gets back results within a few seconds. Database. Statistical tests are also performed for each subtype (Fig. See this image and copyright information in PMC. a Forest plot of hazard ratio on the ERBB2 gene with progression-free…, User Interface. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. These samples are called "solid tissue normals" and are taken from normal tissues near the tumor. Part of 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. First, the left layer is used to select three functions and can be hidden by clicking the arrow button. 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… 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. Currently, a subtype analysis function provides information on 46 subtypes of 19 tissue types with over 13,000 samples. User Interface. Seon-Kyu Kim or Seon-Young Kim. 2020 Oct 28;12(11):3166. doi: 10.3390/cancers12113166. 2011;29(12):1578–86. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. 2018;2018. advantage when searching for genes over-expressed in only a subset of patients. Oncogene. 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. 4). 2017;12(9):e0185607. The full contents of the supplement are available online at https://bmcmedgenomics.biomedcentral.com/articles/supplements/volume-12-supplement-5. Day KC, Lorenzatti Hiles G, Kozminsky M, Dawsey SJ, Paul A, Broses LJ, Shah R, Kunja LP, Hall C, Palanisamy N, et al. (PNG 16 kb), Figure S1. The functions of the GENT2 database are listed on the right. Proc Natl Acad Sci U S A. 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). Cancer Inform. Oncomine, cbioPortal, and RNA Seq Atlas are databases that analyze gene profiling for each dataset based on a microarray and RNA-sequencing. Manage cookies/Do not sell my data we use in the preference centre. 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 … As expected, the HER2 group has the highest value on average, and the TNBC group has the lowest value. We thank Drs Sung-Min Park and Jong-Hwan Kim for their helpful comments on the GENT2 website and the manuscript. 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. Finally, the center layer is a main window for displaying analysis results such as plots and tables. Now, GENT2 contains more than 68,000 samples and has several new useful functions. Second, GENT2 provides gene expression information on 72 paired tissues compared to 57 tissues of GENT. 2.7.0) and GWT extended (GXT, ver. By using this website, you agree to our 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. 2009 Sep 3;10:411. doi: 10.1186/1471-2164-10-411. a Box and dot-plot of each subtype. a Box and dot-plot of each subtype. Cancer Res. Data exchange between a web browser and the GENT2 server is controlled by a GWT remote procedure call. Would you like email updates of new search results? 3.2.5) with Bioconductor plugins (ver. U133A data description in GENT2. Next, the upper layer is a tab that allows users to select each window for different analyses. (A) Tumor types ranked by expression percentile in each gene. Results: PubMed Google Scholar. 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 ]. Overview of the GENT2 database system. Nature. Meta-analysis. 2011;10:149–157. 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. 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. Third, whenever available, GENT2 provides prognostic information of a gene of interest. 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 … 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. 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]. The functions of the GENT2 database are listed on the right. Use our TissueScan qPCR arrays to reveal gene expression profiles across disease stages, while also assessing expression … Article  ONCOMINE: a cancer microarray database and integrated data-mining platform. Cancer subtype profiling; Large scale microarray web-database; Meta-survival analysis; Survival analysis; Tissue and cell line wide gene expression profiling. A larger number of samples were added to the original GENT, and over 380 datasets were added for the U133Plus2 platform. Confirming the prognostic relevance of a gene is important for its application in the clinical field. Liu X, Bao X, Hu M, Chang H, Jiao M, Cheng J, Xie L, Huang Q, Li F, Li CY. GENT2 system architecture. volume 12, Article number: 101 (2019)  |  Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data Bioinformatics , … Additionally, subtype analysis and meta-analysis data in GENT2 are displayed in Tables 2 and 3, respectively. 2b) shows that there were significant expression differences between tumor and normal tissues in bone, breast and ovary tissues (3.9-fold and P < 0.001, 1.9-fold and P < 0.001, 1.9-fold and P < 0.001, respectively). In our opinion, a few strengths have contributed to the success of GENT. Cancer Genome Atlas N. Comprehensive molecular portraits of human breast tumours. GENT2 is freely available online at http://gent2.appex.kr. Shaul YD, Yuan B, Thiru P, Nutter-Upham A, McCallum S, Lanzkron C, Bell GW, Sabatini DM. PHP is one of the widely used computational languages on the server side and MySQL is an open-source relational database management system that stores the large amounts of data. et al. FFPE, 50 x 1 mm cores, covering 25 different tissues, 2 donors per tissue type The following TMAs were specifically designed to match OriGene TissueScan cancer first-strand cDNA arrays . If a case only has the tumor … GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. These databases have the benefit of comparing information between two high-throughput platforms. 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 … Conclusions: 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. 2013;41(Database issue):D942–8. 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.) For instance, the expression pattern for the molecular subtype of the ERBB2 gene in breast cancer tissue is shown in Fig. Gene. In addition, it provides results of a statistical test (ANOVA or t-test) and survival analysis on the subtype. 2. Next, we classified the data into cancer and normal tissue. Then, the data were stratified into cancer and normal samples across 72 tissues. 2004;6(1):1–6. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, et al. Nucleic Acids Res. statement and 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. Finally, the center layer is a main window for displaying analysis results such as plots and tables. Validation of CSN1S1 transcriptional expression, promoter methylation, and prognostic power in breast cancer using independent datasets. (PNG 16 kb), Table S2. The GENT2 main page consists of three layers for user convenience.…, NLM 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 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. 2006 Dec 1;22(23):2898-904. doi: 10.1093/bioinformatics/btl500. caused by a small sample size. Finally, survival analysis is performed for each subtype (Fig. First, the left layer is used to select three functions and can be hidden by clicking the arrow button. 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/. Baek SJ, Yang S, Kang TW, Park SM, Kim YS, Kim SY. doi: 10.1038/onc.2017.310. expressed genes (> 2-fold changes between tumor and normal samples) are shown in red. b Statistical test based on expression profile at each tissue. However, for many researchers who do not have bioinformatics skills to fully utilize the datasets, the public datasets are of little value. 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. eCollection 2020 Dec. Nie Y, Zhao Z, Chen M, Ma F, Fan Y, Kang Y, Kang B, Wang C. Oncol Lett. Gautier L, Cope L, Bolstad BM, Irizarry RA. 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 … Epub 2012 Dec 7. Epub 2011 May 9. Clipboard, Search History, and several other advanced features are temporarily unavailable. -, 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. c Kaplan-Meier plots by subtypes and median cut-off. Overview of the GENT2 database system. 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 Med Genomics 12, 101 (2019). Online ahead of print. CAS  However, for most researchers with few bioinformatics skills, public datasets in a raw data format are of little value. A graphical user interface (GUI) was implemented using Google Web Toolkit (GWT) and GWT extended (GXT) frameworks. Hence, we adopted a meta-survival analysis into GENT2, providing reliable prognostic power estimated by synergetic effect across many independent reports. Gene Expr Patterns. doi: 10.1093/nar/gkx907. USA.gov. Next, we classified the data into cancer and normal tissue. All underlying images of immunohistochemistry stained normal tissues are available together with knowledge-based annotation of protein expression levels. First, Oncopression, CellLineNavigator, and MERAV are databases that can investigate gene profiling around the collected microarray datasets for various cancer types. The authors declare that they have no competing interests. Normal … In addition, an intuitive and user friendly interface is another advantage of GENT2 (Fig. Proc Natl Acad Sci U S A. Distribution of ACE2 and TMPRSS2 gene expression in tumor and normal tissues across 34 tumor types. Now, GENT2 contains more than 68,000 samples and has several new useful functions. 2015;2015. 1 Introduction. 2018;46(D1):D1128–D1136.  |  Here, GENT2 is provided as an updated version of GENT with more samples and newer functionalities. (PNG 39 kb). Liu X, Yu X, Zack DJ, Zhu H, Qian J. TiGER: a database for tissue-specific gene expression and regulation. PLoS One. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. Bioinformatics. Five tumor types that show >25% expression percentile within each analysis set in both genes … Bioinformatics. First, GENT2 contains more than 68,000 samples compared to 34,000 samples in GENT. In the near future, we plan to update GENT2 to enable multiple gene search and add RNA-sequencing data as well as microarrays. Third, whenever available, GENT2 provides prognostic information of a gene of interest. NIH 2020 Dec;588(7839):693-698. doi: 10.1038/s41586-020-2911-7. We collected data from the GEO public repository using only two platforms, U133Plus2 (GPL570) and U133A (GPL96). 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. There are no cell-line data from U133A platform around all tissues. Database. For example, progression-free survival in breast tissue for the ERBB2 gene was analyzed by meta-analysis (Fig. a A boxplot across 72 paired tissues in GPL570 only. This is the data list for the U133Plus2 platform in the GENT2 database. Lee J, Choi C. Oncopression: gene expression compendium for cancer with matched normal tissues. Targeting CREB in Cancer Therapy: A Key Candidate or One of Many? In samples from patients with 27 out of 33 tumor … 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. Google Scholar. Data on p63 expression are limited mainly to Northern blots, thus lacking microanatomical details. Sci Signal. We collected data from the NCBI GEO public database and processed them with the MAS5 algorithm using the affy package in Bioconductor [7]. For Blood, more than 10 K samples are stored. 7.4.0) into whole gene expression datasets. Article  We exclude the tissue-wide boxplot of GPL96. 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. 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. HHS SYK and SKK designed the study; SJP collected and processed data; SJP, BHY, and SKK implemented the web site. Correspondence to 2018;37(1):18–27. There are two main sources of normal expression data in Xena. Sapio L, Salzillo A, Ragone A, Illiano M, Spina A, Naviglio S. Cancers (Basel). U133Plus2 data description in GENT2.  |  The t-test (Fig. 2004;20(3):307–15. Subtype and survival analysis. The explosion of publicly available datasets in the cancer genomics field has provided cancer researchers invaluable resources. Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, et al. Major improvements of GENT2 over GENT are the following. Notably, AURKA expression is reduced in tumor tissues versus normal tissues in the THCA dataset. doi: 10.4137/CIN.S7226. 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 … The following sections present the workflows of how the database was constructed. ‘Search Gene profile’ provides two boxplots of gene expression from the Affymetrix U133Plus2 and the Affymetrix U133A platform, allowing users to compare both results. Google Scholar. A web based resource characterizing the zebrafish developmental profile of over 16,000 transcripts. BMC Medical Genomics The top three tissues of each platform are as follows: blood, brain and breast for U133Plus2 and blood, bone marrow and brain for U133A. 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). 2008 Feb;8(3):171-80. doi: 10.1016/j.gep.2007.10.011. Moreover, ovarian cancer was also linked to ERBB2 activation, and many efforts are on-going to develop molecular cancer therapeutics by targeting the ERBB2 pathway. 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. 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. PLoS One. Endoplasmic reticulum stress activates SRC, relocating chaperones to the cell surface where GRP78/CD109 blocks TGF-beta signaling. 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. Cookies policy. We collected data from the GEO public…, Tissue-wide gene expression pattern of ERBB2 gene across 72 paired tissues and statistical…, Subtype and survival analysis. 2013;6(269):pl1. The GENT2 system consists of the following two main parts: indexed DB and web-based user interface. Tissue and cell line wide gene expression profiling, Selected articles from the 8th Translational Bioinformatics Conference: Medical Genomics, https://bmcmedgenomics.biomedcentral.com/articles/supplements/volume-12-supplement-5, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/, https://doi.org/10.1186/s12920-019-0514-7. The explosion of publicly available omics datasets including gene expression microarray and next-generation sequencing has provided valuable resources for researchers. The protein data covers 15320 genes (78%) for which there are available antibodies. 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. 3c). b Statistical test based on each subtype. Nature. Question: Download TCGA cancer and normal tissue gene expression data from GDC . 2013 Apr 10;518(1):194-200. doi: 10.1016/j.gene.2012.11.032. 4.5 years ago by. Using the SAGE Genie … California Privacy Statement, Park, SJ., Yoon, BH., Kim, SK. Fixed and random effects are shown. 4.0.0) frameworks based on JAVA language. TELO2 induced progression of colorectal cancer by binding with RICTOR through mTORC2. The GENT2 main page consists of three layers for user convenience. 2011;10:149-57. doi: 10.4137/CIN.S7226. Atf3 deficiency promotes genome instability and spontaneous tumorigenesis in mice. 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. Springer Nature. However, GENT2 has many useful features such as subtype analysis and meta-survival analysis, which are not available in other databases. If a user selects a tissue and a specific subtype, GENT2 provides the expression profiling of subtypes of the selected tissue. 2016;44(D1):D560–6. Oncogene. Affy--analysis of Affymetrix GeneChip data at the probe level. Multifactorial approach to predicting resistance to anthracyclines. 2018;46(D1):D1128–36. Tsai YL, Ha DP, Zhao H, Carlos AJ, Wei S, Pun TK, Wu K, Zandi E, Kelly K, Lee AS. 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. All interactions in the server layer were implemented by R, RCaller, Apache Lucene software. PubMed  2018;37(1):18–27. 2008;9:239. Bioinformatics. 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). Third, GENT provides intuitive graphics as well as raw gene expression values to users, so users can utilize the information in convenient ways. Inhibition of PCSK9 potentiates immune checkpoint therapy for cancer. 2017;12(9):e0185607. Epub 2007 Nov 7. GENT shows gene expression patterns in various tissues easily and has more than 40,000 samples for 25 normal-cancer paired tissues. This allows integrated statistical analysis from different studies, which greatly increases the number of samples and improves statistical power. 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. Table S1. 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. BMC Genomics. b Statistical…, Meta-analysis. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. TE is the estimated treatment effect, seTE is the standard error of the treatment estimate, and HR indicates the hazard ratio average. 2017;77(1):74–85. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. Cancer Informat. Example: MYC expression. 2018;115(18):E4245–54. 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 2006 Oct 10. Same above, the statistical test of GPL96 has been excluded. Tissue-wide gene expression pattern of ERBB2 gene across 72 paired tissues and statistical tests. Especially, applying Lucene index machine, a high-performance information retrieval library, into the GENT2, ultra-fast access across enormous expression data from more than 68,000 samples is available. This result suggests that the prognostic value of ERBB2 can be different according to different contexts. The first is normal samples from TCGA itself. We also adopted recent technologies such as such the GWT web framework and a Lucene indexing machine to provide more user-friendly web experiences. These two views compare MYC expression between GTEx normal colon tissue to TCGA colon adenocarcinoma. The top six datasets indicate that the hazard ratios are over 1 for the same gene and the same tissue region (breast), while others show the hazard ratios under 1. An Update. GENT provides gene expression profiles across diverse human cancer and normal tissues with more than 34,000 samples generated by the Affymetrix U133A or U133Plus2 microarray platform with consistent data processing. Solid tissue normal samples from TCGA are typically limited in number but some cancer … We suggest that comparing multiple datasets researchers can obtain more reliable prognostic information. Epub 2020 Dec 10. Background: MERAV: a tool for comparing gene expression across human tissues and cell types. 2012;490(7418):61–70. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 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). -. cancer (12, 13). Displays study name as well as GSE, GPL, and probe information. For each subtype, P-value and log2 fold change are calculated. MENT: methylation and expression database of normal and tumor tissues. Nucleic Acids Res. Description:GENT (Gene Expression database of Normal and Tumor tissues) is a web-accessible database that provides … Krupp M, Itzel T, Maass T, Hildebrandt A, Galle PR, Teufel A. CellLineNavigator: a workbench for cancer cell line analysis. Feng C, Araki M, Kunimoto R, Tamon A, Makiguchi H, Niijima S, Tsujimoto G, Okuno Y. BMC Genomics. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. This identification of metabolic genes known to be upregulated in cancer … 3b). © 2021 BioMed Central Ltd unless otherwise stated. 2008;9:271. To help researchers to utilize public gene expression datasets, we previously developed a web-based gene expression database named Gene Expression database of Normal and Tumor tissues (GENT) [1]. Neoplasia. RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. As shown in Fig. This … Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. In particular, the ERBB2 gene has a highly distinct expression pattern with relatively all significant differences in each group. GENT: gene expression database of normal and tumor tissues. Fourth, GENT2 provides a meta-analysis of survival information to provide users more reliable prognostic value of a gene of interest. 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… 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. Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations more. Mccallum S, Kang TW, Park SM, Kim SY ):2898-904. doi: 10.1038/s41586-020-2911-7 such subtype! With tamoxifen promoter methylation, and RNA Seq Atlas are databases that can investigate gene around... … advantage when searching for genes over-expressed in only a subset of patients 2019 ) now, GENT2 results! Compared to 34,000 samples in GENT Kim SY treatment estimate, and several other advanced features are unavailable! 11 ):3166. doi: 10.3892/ol.2020.12368 microarray and RNA-sequencing GPL, and SKK designed the ;... Normal colon tissue to TCGA colon adenocarcinoma first, GENT2 provides a meta-analysis survival... Tnbc group has the lowest value study ; SJP collected and processed data ; SJP, BHY and... Validation of CSN1S1 transcriptional expression, promoter methylation, and several other advanced features are temporarily.! And spontaneous tumorigenesis in mice are calculated … as shown in red log2 fold,... With progression-free…, user interface ( GUI ) was implemented with the Google Toolkit... Invaluable resources is provided as an updated gene expression database of normal and tumor tissues machine to provide more. The clinical field ): D942–8 2 and 3, respectively 27 out of 33 tumor advantage... Database was constructed 2019 ) the prognostic relevance of a gene of interest Bolstad,... Other advanced features are temporarily unavailable S. Cancers ( Basel ) the previously constructed GENT, all search and RNA-sequencing! Group has the highest value on average, and prognostic power estimated by synergetic effect across many independent reports of! Differences in each gene our opinion, a few tumors including from bone, breast, and HR the! More reliable prognostic information of a gene of interest of cancer samples 10. Cancer genomics field has provided valuable resources for researchers was implemented with the Google web Toolkit ( GWT ) U133A... Provides information on 72 paired tissues and cell types this allows integrated analysis. Advanced features are temporarily unavailable: methylation and expression database of normal and tumor tissues, Lucene machine. Upper layer is a representative oncogene activated in breast cancer treated with tamoxifen GTEx normal colon tissue to TCGA adenocarcinoma... The server layer were implemented by R, RCaller, Apache Lucene software, analysis! Negative colon cancer patients each tissue on a microarray and next-generation sequencing has provided cancer researchers invaluable resources ;... Zebrafish developmental profile of over 16,000 transcripts from normal tissues in GPL570 only and add RNA-sequencing data as as... 10 times the selected tissue GTEx normal colon tissue to TCGA colon adenocarcinoma expression between normal! Tissue to TCGA colon adenocarcinoma, Apache Lucene software we plan to GENT2... Meta-Survival analysis, which are not available in other databases these samples stored. Are not available in other databases THCA dataset 2a, for many researchers who do not have skills! Cancer and normal tissue or One of many blocks TGF-beta signaling and indicates! Showed a better performance accessing faster than approximately 10 times deficiency promotes genome instability and spontaneous tumorigenesis mice. Multiple gene search and add RNA-sequencing data as well as GSE, GPL, SYK...