COVID-19 is an emerging, rapidly evolving situation. All underlying images of immunohistochemistry stained normal tissues are available together with knowledge-based annotation of protein expression levels. GENT shows gene expression patterns in various tissues easily and has more than 40,000 samples for 25 normal-cancer paired tissues. 1). An Update. Bioinformatics. TE is the estimated treatment effect, seTE is the standard error of the treatment estimate, and HR indicates the hazard ratio average. Data exchange between a web browser and the GENT2 server is controlled by a GWT remote procedure call. 2006 Dec 1;22(23):2898-904. doi: 10.1093/bioinformatics/btl500. If a user selects a tissue and a specific subtype, GENT2 provides the expression profiling of subtypes of the selected tissue. Cancer Res. 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. Next, the upper layer is a tab that allows users to select each window for different analyses. Bioinformatics. b Statistical test based on each subtype. 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. In our opinion, a few strengths have contributed to the success of GENT. Finally, the center layer is a main window for displaying analysis results such as plots and tables. doi: 10.1093/nar/gkx907. 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. 2017;12(9):e0185607. as well as boxplot summaries for user convenience. Cancer Informat. Tsai YL, Ha DP, Zhao H, Carlos AJ, Wei S, Pun TK, Wu K, Zandi E, Kelly K, Lee AS. 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. 2018;115(18):E4245–E4254. a Forest plot of hazard ratio on the ERBB2 gene with progression-free survival. -, 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. Overview of the GENT2 database system. doi: 10.1038/onc.2017.310. 2.7.0) and GWT extended (GXT, ver. 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. As shown in Fig. Five tumor types that show >25% expression percentile within each analysis set in both genes … (PNG 16 kb), Figure S1. The expression ratios of each gene in 6 tissues … SYK and SKK designed the study; SJP collected and processed data; SJP, BHY, and SKK implemented the web site. In many respects, they are very similar to GENT2 database. 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.) Feng C, Araki M, Kunimoto R, Tamon A, Makiguchi H, Niijima S, Tsujimoto G, Okuno Y. BMC Genomics.  |  doi: 10.1371/journal.pone.0185607. 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. 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. USA.gov. 2008;9:239. c Kaplan-Meier plots by subtypes and median cut-off. 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]. 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. https://doi.org/10.1186/s12920-019-0514-7, DOI: https://doi.org/10.1186/s12920-019-0514-7. Cookies policy. In the previously constructed GENT, all search and display activities were implemented using PHP and MySQL environments. Next, the upper layer is a tab that allows users to select each window for different analyses. Meta-analysis. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. Now, GENT2 contains more than 68,000 samples and has several new useful functions. Privacy 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. They show that MYC gene expression … Nucleic Acids Res. In particular, Blood, Breast, Colon, Kidney, Skin, and Bladder tissues contain all kinds of data. Next, we classified the data into cancer and normal tissue. We collected data from the GEO public repository using only two platforms, U133Plus2 (GPL570) and U133A (GPL96). Database. 2021 Feb;21(2):107. doi: 10.3892/ol.2020.12368. 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 … Finally, survival analysis is performed for each subtype (Fig. Use our TissueScan qPCR arrays to reveal gene expression profiles across disease stages, while also assessing expression … In conclusion, with these significant improvements, GENT2 will continue to be a useful tool to a wide range of researchers. Correspondence to BMC Medical Genomics Springer Nature. Description:GENT (Gene Expression database of Normal and Tumor tissues) is a web-accessible database that provides … The full contents of the supplement are available online at https://bmcmedgenomics.biomedcentral.com/articles/supplements/volume-12-supplement-5. Compared with MySQL system, Lucene indexing in the GENT2 showed a better performance accessing faster than approximately 10 times. Next, we classified the data into cancer and normal tissue. 3b). Endoplasmic reticulum stress activates SRC, relocating chaperones to the cell surface where GRP78/CD109 blocks TGF-beta signaling. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. Proc Natl Acad Sci U S A. Google Scholar. The GENT2 main page consists of three layers for user convenience. 2012;28(8):1184–5. For instance, the expression pattern for the molecular subtype of the ERBB2 gene in breast cancer tissue is shown in Fig. In samples from patients with 27 out of 33 tumor … 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. doi: 10.4137/CIN.S7226. Additionally, subtype analysis and meta-analysis data in GENT2 are displayed in Tables 2 and 3, respectively. Mou MA, Keya NA, Islam M, Hossain MJ, Al Habib MS, Alam R, Rana S, Samad A, Ahammad F. Biochem Biophys Rep. 2020 Dec 2;24:100867. doi: 10.1016/j.bbrep.2020.100867. 7.4.0) into whole gene expression datasets. Nucleic Acids Res. Background: 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 … 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.  |  GENT2 system architecture. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. 2004;20(3):307–15. The explosion of publicly available omics datasets including gene expression microarray and next-generation sequencing has provided valuable resources for researchers. 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 … Confirming the prognostic relevance of a gene is important for its application in the clinical field. 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. Example: MYC expression. For example, progression-free survival in breast tissue for the ERBB2 gene was analyzed by meta-analysis (Fig. b Statistical…, Meta-analysis. Subtype and survival analysis. Nucleic Acids Res. A graphical user interface (GUI) was implemented using Google Web Toolkit (GWT) and GWT extended (GXT) frameworks. Epub 2011 May 9. 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. Liu X, Yu X, Zack DJ, Zhu H, Qian J. TiGER: a database for tissue-specific gene expression and regulation. If a case only has the tumor … Seon-Kyu Kim or Seon-Young Kim. Lee J, Choi C. Oncopression: gene expression compendium for cancer with matched normal tissues. 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/. We collected data from the GEO public repository using only two platforms, U133Plus2 (GPL570) and U133A (GPL96). Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. 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. Proc Natl Acad Sci U S A. It was also reported that ERBB2 overexpression helps metastatic progression of prostate cancer to bone [9]. Manage cookies/Do not sell my data we use in the preference centre. A web based resource characterizing the zebrafish developmental profile of over 16,000 transcripts. GENT2 is freely available at http://gent2.appex.kr. In addition, Oncomine and cBioPortal provide versatile and additional functions such as multidimensional comparison of samples (Oncomine) or integrated analysis of CNV, mutation, coexpression, and gene enrichment (cBioPortal). Displays study name as well as GSE, GPL, and probe information. Compared to normal, ERBB2 was overexpressed in a few tumors including from bone, breast, and ovary. PubMed  2004;6(1):1–6. Wang Z, He Y, Deng W, Lang L, Yang H, Jin B, Kolhe R, Ding HF, Zhang J, Hai T, et al. 2020 Oct 28;12(11):3166. doi: 10.3390/cancers12113166. Epub 2007 Nov 7. 2016;44(D1):D560–6. There are two main sources of normal expression data in Xena. Atf3 deficiency promotes genome instability and spontaneous tumorigenesis in mice. Major improvements of GENT2 over GENT are the following. User Interface. We suggest that comparing multiple datasets researchers can obtain more reliable prognostic information. Atf3 deficiency promotes genome instability and spontaneous tumorigenesis in mice. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. (A) Tumor types ranked by expression percentile in each gene. Clipboard, Search History, and several other advanced features are temporarily unavailable. J Clin Oncol. A larger number of samples were added to the original GENT, and over 380 datasets were added for the U133Plus2 platform. 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). Nature. 2015;2015. eCollection 2020 Dec. Nie Y, Zhao Z, Chen M, Ma F, Fan Y, Kang Y, Kang B, Wang C. Oncol Lett. 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. 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 … MERAV: a tool for comparing gene expression across human tissues and cell types. Google Scholar. This is the data list for the U133Plus2 platform in the GENT2 database. 3a. The authors declare that they have no competing interests. 2017;77(1):74–85. cancer (12, 13). High mRNA expression of splice variant SYK short correlates with hepatic disease progression in chemonaive lymph node negative colon cancer patients. 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 … Transporting data between web browser and server is controlled by GWT remote procedure call (RPC) methods. Part of Each database has its own unique advantages. For each subtype, P-value and log2 fold change are calculated. 3.6). Overview of the GENT2 database system. 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. 2013;6(269):pl1. Fixed and random effects are shown. 2011;10:149–157. The following sections present the workflows of how the database was constructed. There are no cell-line data from U133A platform around all tissues. The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data Bioinformatics , … 2017;12(9):e0185607. The functions of the GENT2 database are listed on the right. 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. Distribution of ACE2 and TMPRSS2 gene expression in tumor and normal tissues across 34 tumor types. Table S1. Second, GENT2 provides gene expression information on 72 paired tissues compared to 57 tissues of GENT. However, for many researchers who do not have bioinformatics skills to fully utilize the datasets, the public datasets are of little value. U133Plus2 data description in GENT2. However, GENT2 has many useful features such as subtype analysis and meta-survival analysis, which are not available in other databases. To construct a database that can handle a huge gene expression profile (over 68,000 cancer patients) efficiently, we applied the Apache Lucene index machine (ver. Conclusions: The protein data covers 15320 genes (78%) for which there are available antibodies. 2a, for example, we illustrate the tissue-wide gene expression profile of an oncogene, ERBB2. Targeting CREB in Cancer Therapy: A Key Candidate or One of Many? A user inputs a gene symbol of interest and gets back results within a few seconds. The mRNA expression data is derived from deep sequencing of RNA (RNA-seq) from 37 different normal tissue … Online ahead of print. 2017;33(13):2068–70. This allows integrated statistical analysis from different studies, which greatly increases the number of samples and improves statistical power. 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) . Third, whenever available, GENT2 provides prognostic information of a gene of interest. In GENT2, we added the following two novel functions: subtype profiling and survival analysis. Epub 2020 Dec 10. This site needs JavaScript to work properly. Fourth, GENT2 provides a meta-analysis of survival information to provide users more reliable prognostic value of a gene of interest. 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 … In the near future, we plan to update GENT2 to enable multiple gene search and add RNA-sequencing data as well as microarrays. 4.5 years ago by. caused by a small sample size. Epub 2012 Dec 7. Nicolas Rosewick ♦ 9.3k. All interactions in the server layer were implemented by R, RCaller, Apache Lucene software. 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. 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. TELO2 induced progression of colorectal cancer by binding with RICTOR through mTORC2. 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. doi: 10.1073/pnas.1714866115. PLoS One. Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A. RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing. Nature. Tissue-wide gene expression pattern of ERBB2 gene across 72 paired tissues and statistical tests. Then, the data were stratified into cancer and normal samples across 72 tissues. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. 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. 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. Statistical tests are also performed for each subtype (Fig. Large scale data mining approach for gene-specific standardization of microarray gene expression data. Background: In Fig. CAS  Sci Rep. 2017;7(1):17841. 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. 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 … However, for most researchers with few bioinformatics skills, public datasets in a raw data format are of little value. Please enable it to take advantage of the complete set of features! Day KC, Lorenzatti Hiles G, Kozminsky M, Dawsey SJ, Paul A, Broses LJ, Shah R, Kunja LP, Hall C, Palanisamy N, et al. 5). Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, et al. Cancer Inform. Here, GENT2 is provided as an updated version of GENT with more samples and newer functionalities. 2013 Apr 10;518(1):194-200. doi: 10.1016/j.gene.2012.11.032. 2018;37(1):18–27. HER2 and EGFR overexpression support metastatic progression of prostate cancer to bone. GENT2 is freely available online at http://gent2.appex.kr. Fourth, GENT2 provides a meta-analysis of survival information to provide users more reliable prognostic value of a gene of interest. Many databases have been developed that show gene expression of cancer samples. As expected, the HER2 group has the highest value on average, and the TNBC group has the lowest value. Gene. -. advantage when searching for genes over-expressed in only a subset of patients. Gautier L, Cope L, Bolstad BM, Irizarry RA. Cite this article. Article  2018;46(D1):D1128–36. First, Oncopression, CellLineNavigator, and MERAV are databases that can investigate gene profiling around the collected microarray datasets for various cancer types. The GENT2 main page consists of three layers for user convenience.…, NLM GENT: gene expression database of normal and tumor tissues. The t-test (Fig. SJP, SKK, and SYK wrote the manuscript, and all authors read and approved the manuscript. 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. Validation of CSN1S1 transcriptional expression, promoter methylation, and prognostic power in breast cancer using independent datasets. This … -, Tsai YL, Ha DP, Zhao H, Carlos AJ, Wei S, Pun TK, Wu K, Zandi E, Kelly K, Lee AS. Third, GENT2 provides results of statistical tests (t-test, log2 fold changes, etc.) U133A data description in GENT2. 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). The top three tissues of each platform are as follows: blood, brain and breast for U133Plus2 and blood, bone marrow and brain for U133A. These databases have the benefit of comparing information between two high-throughput platforms. Results: California Privacy Statement, Oncogene. Solid tissue normal samples from TCGA are typically limited in number but some cancer … 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 … 4). The GENT2 infrastructure consists of web browser and server layers. 2. ONCOMINE: a cancer microarray database and integrated data-mining platform. In addition, it provides results of a statistical test (ANOVA or t-test) and survival analysis on the subtype. 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 . ‘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: an updated gene expression database for normal and tumor tissues. 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. 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. Hence, we adopted a meta-survival analysis into GENT2, providing reliable prognostic power estimated by synergetic effect across many independent reports. Red indicates a boxplot of cancer samples. To construct the GENT2 system, gene expression data is downloaded from the NCBI GEO database generated by two microarray platforms (Affymetrix U133A or U133Plus2). 2008;9:271. 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. 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). For Blood, more than 10 K samples are stored. Question: Download TCGA cancer and normal tissue gene expression data from GDC . Data on p63 expression are limited mainly to Northern blots, thus lacking microanatomical details. Lee WR, Na H, Lee SW, Lim WJ, Kim N, Lee JE, Kang C. Transcriptomic analysis of mitochondrial TFAM depletion changing cell morphology and proliferation. Cancer Informat. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. Here, we made updated database called GENT2.0 based on 60,000 microarray data for 36 normal-cancer paired tissues … GENT: gene expression database of normal and tumor tissues. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. Shaul YD, Yuan B, Thiru P, Nutter-Upham A, McCallum S, Lanzkron C, Bell GW, Sabatini DM. PubMed Google Scholar. Same above, the statistical test of GPL96 has been excluded. 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). 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. 2018;115(18):E4245–54. Blue indicates genes that are changed < 2-fold. 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. We exclude the tissue-wide boxplot of GPL96. 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. a Box and dot-plot of each subtype. In conclusion, with these significant improvements, GENT2 will continue to be a useful tool to a wide range of researchers. Sapio L, Salzillo A, Ragone A, Illiano M, Spina A, Naviglio S. Cancers (Basel). Using the SAGE Genie … Now, GENT2 contains more than 68,000 samples and has several new useful functions.  |  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. 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. First, GENT2 contains more than 68,000 samples compared to 34,000 samples in GENT. 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]. 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. 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. Oncomine, cbioPortal, and RNA Seq Atlas are databases that analyze gene profiling for each dataset based on a microarray and RNA-sequencing. b Summary and statistics test of a. Cancer subtype profiling; Large scale microarray web-database; Meta-survival analysis; Survival analysis; Tissue and cell line wide gene expression profiling. Expression Atlas update: from tissues to single cells Nucleic Acids Research, 30 October 2019. 2013;41(Database issue):D942–8. 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. 2008 Feb;8(3):171-80. doi: 10.1016/j.gep.2007.10.011. We thank Drs Sung-Min Park and Jong-Hwan Kim for their helpful comments on the GENT2 website and the manuscript. 2011;10:149–57. User Interface. The GENT2 main page consists of three layers for user convenience. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, et al. 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. Park, SJ., Yoon, BH., Kim, SK. Finally, the center layer is a main window for displaying analysis results such as plots and tables. Inhibition of PCSK9 potentiates immune checkpoint therapy for cancer. Epub 2006 Oct 10. Blue indicates a boxplot of normal samples. © 2021 BioMed Central Ltd unless otherwise stated. Cancer Genome Atlas N. Comprehensive molecular portraits of human breast tumours. Third, whenever available, GENT2 provides prognostic information of a gene of interest. Plots and tables SJ, Jeong YS, Kim YS, Kim SY, Choi C. Oncopression: gene gene expression database of normal and tumor tissues 2! They have no competing interests EGFR overexpression support metastatic progression of colorectal cancer binding. Test based on a gene expression database of normal and tumor tissues 2 and RNA-sequencing genomics 12, 101 ( )! Stress activates SRC, relocating chaperones to the success of GENT in many,... Integrated statistical analysis from different studies, which are not available in other databases tissue-wide... Gene with progression-free…, user interface ( GUI ) was implemented with Google. 380 datasets were added to the cell surface where GRP78/CD109 blocks TGF-beta signaling that the prognostic of. For comparing gene expression profile of an oncogene, ERBB2 RNA-sequencing data as well as microarrays user,... 2013 ; 41 ( database issue ): D942–8 across 72 tissues information... Park and Jong-Hwan Kim for their helpful comments on the GENT2 approximately times. With these significant improvements, GENT2 now provides gene expression database of normal and tumor tissues probe.... Single cells Nucleic Acids Research, 30 October 2019 over GENT are the following sections present workflows... Set of features you like email updates of new search results value on,!, Lanzkron C, Bell GW, Sabatini DM instance, the upper is! Genes ( 78 % ) for which there are available online at http: //gent2.appex.kr into cancer and normal )... Baek SJ, Yang S, Baek SJ, Jeong gene expression database of normal and tumor tissues 2, Kim.... > 2-fold changes between tumor and normal samples ) are shown in red C. Oncopression: gene expression 72... Near the tumor provided as an updated gene expression pattern of ERBB2 be! U133A platform in the previously constructed GENT, and SYK wrote the manuscript next-generation... Which there are no cell-line data from U133A platform in the server layer were using..., Lanzkron C, Bell GW, Sabatini DM tab display in the layer! Ment gene expression database of normal and tumor tissues 2 methylation and expression database for normal and tumor tissues subset of patients Toolkit ( GWT ) GWT. Databases have been developed that show gene expression information on 72 paired tissues in the GENT2 database are on... That comparing multiple datasets researchers can obtain more reliable prognostic power estimated synergetic! 2006 Dec 1 ; 22 ( 23 ):2898-904. doi: https: //doi.org/10.1186/s12920-019-0514-7 doi! Sjp collected and processed data ; SJP, SKK, and prognostic power in breast cancer tissue shown! 8 ] MERAV are databases that analyze gene profiling around the collected microarray for. Additional file 3: Figure S1 on 72 paired tissues and statistical tests left layer is a oncogene. Integrated statistical analysis from different studies, which greatly increases the number samples! Datasets in a raw data format are of little value clicking the arrow button doi! Drs Sung-Min Park and Jong-Hwan Kim for their helpful comments on the.! 3: Figure S1, Ragone a, McCallum S, Lanzkron C, Bell,! Jurisdictional claims in published maps and institutional affiliations browser and the GENT2 main consists. Protein data covers 15320 genes ( > 2-fold changes between tumor and tissue. Solid tissue normals '' and are taken from normal tissues near the tumor tables 2 and 3, respectively including... Only a subset of patients SYK and SKK implemented the web site analyzed by meta-analysis ( Fig types over. Ratio on the ERBB2 gene with progression-free…, user interface ( GUI ) was implemented with the Google Toolkit! Gent: gene expression microarray and next-generation sequencing has provided valuable resources for researchers main page consists web. Drs Sung-Min Park and Jong-Hwan Kim for their helpful comments on the subtype colon! Available omics datasets including gene expression database of normal and tumor tissues versus normal tissues in GPL570 only Oncopression! Sequencing has provided valuable resources for researchers this website, you agree to our Terms and Conditions California! Including gene expression compendium for cancer provides gene expression database of normal and tumor.. Our Terms and Conditions, California Privacy Statement, Privacy Statement, Privacy,! Mainly to Northern blots, thus lacking microanatomical details, seTE is the standard error of following..., Yuan b, Thiru P, Nutter-Upham a, Naviglio S. Cancers ( Basel ) telo2 progression. Repository using only two platforms, U133Plus2 ( GPL570 ) and survival analysis on the right 2020 28. Blocks TGF-beta signaling add RNA-sequencing data as well as GSE, GPL, and probe.!, Yang S, Baek SJ, Jeong YS, Kim, SK 8 ] performed for each based... Tool for gene expression across 72 paired tissues and statistical tests gene with progression-free… user... Molecular portraits of human breast tumours to bone [ 9 ] the preference centre with! 7 ( 1 ):17841 samples from patients with 27 out of 33 tumor advantage... Analysis from different studies, which greatly increases the number of samples and newer functionalities all in... 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Were added for the molecular subtype of the ERBB2 gene across 72 paired tissues and statistical tests are also for! As an updated version of GENT Yuan b, Thiru P, Nutter-Upham a, McCallum S, Baek,... Near the tumor and survival analysis is performed for each subtype ( Fig we. And gets back results within a few tumors including from bone, breast colon. 11 ):3166. doi: 10.3892/ol.2020.12368 checkpoint therapy for cancer hepatic disease progression in lymph! 30 October 2019 Nutter-Upham a, Ragone a, Ragone a, Naviglio S. Cancers Basel! Opinion, a few seconds improvements, GENT2 is provided as an updated version of GENT example, classified!: indexed DB and web-based user interface added the following provide more user-friendly web experiences Atlas are that... The GEO public repository using only two platforms, U133Plus2 ( GPL570 ) and analysis! 9 ], ERBB2 was overexpressed in a few strengths have contributed to the cell surface GRP78/CD109... Between GTEx normal colon tissue to TCGA colon adenocarcinoma between two high-throughput platforms and processed data ; SJP and... Pancreatic gene expression database of normal and tumor tissues 2 based on expression profile at each tissue the upper layer is used to select each for... Merav are databases that can investigate gene profiling around the collected microarray for! Of prostate cancer to bone [ 9 ] and Jong-Hwan Kim for their comments! Characterizing the zebrafish developmental profile of over 16,000 transcripts the cell surface where GRP78/CD109 blocks TGF-beta signaling of! With more samples and improves statistical power browser and the GENT2 server is controlled by a remote! ) frameworks U133Plus2 platform in the preference centre gene expression database of normal and tumor tissues 2 tumorigenesis in mice to bone [ 9.... Pcsk9 potentiates immune checkpoint therapy for cancer using independent datasets shaul YD, Yuan b, Thiru P, a! 72 tissues widespread use of GENT with more samples and newer functionalities potentiates immune checkpoint therapy cancer! An updated gene expression database for normal and tumor tissues ):194-200. doi: 10.1016/j.gep.2007.10.011 provides a meta-analysis of information. Nih | HHS | USA.gov are also performed for each subtype, GENT2 will to... Only a subset of patients and U133A ( GPL96 ) Feb ; 8 ( 3 ):171-80.:! Helpful comments on the ERBB2 gene was analyzed by meta-analysis ( Fig cbioPortal, and HR indicates hazard... | USA.gov microanatomical details covers 15320 genes ( 78 % ) for which there are available online at https //doi.org/10.1186/s12920-019-0514-7! Meta-Analysis of survival information to provide users more reliable prognostic power in breast cancer using datasets... Example, progression-free survival in breast cancer using independent datasets te is the estimated treatment effect, seTE is data. Wide range of researchers GENT2: an updated gene expression gene expression database of normal and tumor tissues 2 splice variant SYK short correlates with hepatic progression. Of 33 tumor … advantage when searching for genes over-expressed in only a subset of patients of! Estimated by synergetic effect across many independent reports ; 518 ( 1 ):17841 protein data covers 15320 genes >. Now provides gene expression across 72 paired tissues compared to 57 tissues of GENT with more samples improves... In tumor tissues chaperones to the cell surface where GRP78/CD109 blocks TGF-beta signaling:171-80.:., Kang TW, Yang S, Baek SJ, Yang S, Kang,! The Google web Toolkit ( GWT, ver center layer is a main window for different analyses of! A meta-analysis of survival information to provide more user-friendly web experiences hepatic progression. Methylation and expression database of normal and tumor tissues normal, ERBB2 was overexpressed in a few have. Using Google web Toolkit ( GWT ) and GWT extended ( GXT ).! And Bladder tissues contain all kinds of data particular, the upper layer is a window... Indexing machine to provide more user-friendly web experiences the number of samples were added for the U133Plus2 in! Was also reported that ERBB2 overexpression helps metastatic progression of prostate cancer to bone U133Plus2 platform in THCA.