gene expression database of normal and tumor tissues 2

2018;115(18):E4245–54. In many respects, they are very similar to GENT2 database. Manage cookies/Do not sell my data we use in the preference centre. 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. In conclusion, with these significant improvements, GENT2 will continue to be a useful tool to a wide range of researchers. Proc Natl Acad Sci U S A. However, for many researchers who do not have bioinformatics skills to fully utilize the datasets, the public datasets are of little value. 2004;6(1):1–6. Distribution of ACE2 and TMPRSS2 gene expression in tumor and normal tissues across 34 tumor types. The GENT2 system consists of the following two main parts: indexed DB and web-based user interface. Nucleic Acids Res. First, the left layer is used to select three functions and can be hidden by clicking the arrow button. U133A data description in GENT2. Major improvements of GENT2 over GENT are the following. 2017;77(1):74–85. as well as boxplot summaries for user convenience. Belgium, Brussels. PLoS One. The system architecture of GENT2 is illustrated in Additional file 3: Figure S1. 2020 Oct 28;12(11):3166. doi: 10.3390/cancers12113166. MENT: methylation and expression database of normal and tumor tissues. 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 … Affy--analysis of Affymetrix GeneChip data at the probe level. J Clin Oncol. 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. Online ahead of print. See this image and copyright information in PMC. 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. GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. 2018;37(1):18–27. 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/. PLoS One. In conclusion, with these significant improvements, GENT2 will continue to be a useful tool to a wide range of researchers. Epub 2011 May 9. Seon-Kyu Kim or Seon-Young Kim. 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. 3.2.5) with Bioconductor plugins (ver. The functions of the GENT2 database are listed on the right. Sci Rep. 2017;7(1):17841. First, Oncopression, CellLineNavigator, and MERAV are databases that can investigate gene profiling around the collected microarray datasets for various cancer types. Transporting data between web browser and server is controlled by GWT remote procedure call (RPC) methods. Here, we made updated database called GENT2.0 based on 60,000 microarray data for 36 normal-cancer paired tissues … For each subtype, P-value and log2 fold change are calculated. 2006 Dec 1;22(23):2898-904. doi: 10.1093/bioinformatics/btl500. The GENT2 infrastructure consists of web browser and server layers. Confirming the prognostic relevance of a gene is important for its application in the clinical field. 2012;490(7418):61–70. GENT shows gene expression patterns in various tissues easily and has more than 40,000 samples for 25 normal-cancer paired tissues. 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 … Park, SJ., Yoon, BH., Kim, SK. Use our TissueScan qPCR arrays to reveal gene expression profiles across disease stages, while also assessing expression … All underlying images of immunohistochemistry stained normal tissues are available together with knowledge-based annotation of protein expression levels. 2013;41(Database issue):D942–8. 2008;9:271. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM.  |  First, GENT2 contains more than 68,000 samples compared to 34,000 samples in GENT. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. 2017;12(9):e0185607. Here, GENT2 is provided as an updated version of GENT with more samples and newer functionalities. 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. -, Tsai YL, Ha DP, Zhao H, Carlos AJ, Wei S, Pun TK, Wu K, Zandi E, Kelly K, Lee AS. 2004;20(3):307–15. statement and 2013 Apr 10;518(1):194-200. doi: 10.1016/j.gene.2012.11.032. (A) Tumor types ranked by expression percentile in each gene. 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.) 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. Red indicates a boxplot of cancer samples. 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]. Now, GENT2 contains more than 68,000 samples and has several new useful functions. The mRNA expression data is derived from deep sequencing of RNA (RNA-seq) from 37 different normal tissue … 5). In the near future, we plan to update GENT2 to enable multiple gene search and add RNA-sequencing data as well as microarrays. Nature. doi: 10.1073/pnas.1714866115. c Kaplan-Meier plots by subtypes and median cut-off. Epub 2012 Dec 7. 4.5 years ago by. 2018;115(18):E4245–E4254. Epub 2006 Oct 10. 2. Shin G, Kang TW, Yang S, Baek SJ, Jeong YS, Kim SY. 7.4.0) into whole gene expression datasets. SYK and SKK designed the study; SJP collected and processed data; SJP, BHY, and SKK implemented the web site. 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). This is the data list for the U133Plus2 platform in the GENT2 database. BMC Med Genomics 12, 101 (2019). Endoplasmic reticulum stress activates SRC, relocating chaperones to the cell surface where GRP78/CD109 blocks TGF-beta signaling. Third, GENT2 provides results of statistical tests (t-test, log2 fold changes, etc.) Finally, GENT2 provides results of meta-survival analysis combining various independent studies for reliable prognostic information. 2016;44(D1):D560–6. In samples from patients with 27 out of 33 tumor … Cancer subtype profiling; Large scale microarray web-database; Meta-survival analysis; Survival analysis; Tissue and cell line wide gene expression profiling. 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. Results: Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, et al. Table S1. The following sections present the workflows of how the database was constructed. (PNG 16 kb), Figure S1. 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]. A graphical user interface (GUI) was implemented using Google Web Toolkit (GWT) and GWT extended (GXT) frameworks. a Forest plot of hazard ratio on the ERBB2 gene with progression-free…, User Interface.  |  Guo Z, Zhang X, Zhu H, Zhong N, Luo X, Zhang Y, Tu F, Zhong J, Wang X, He J, Huang L. Oncol Rep. 2020 Dec 9;45(2):523-34. doi: 10.3892/or.2020.7890. Hence, we adopted a meta-survival analysis into GENT2, providing reliable prognostic power estimated by synergetic effect across many independent reports. 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 … TELO2 induced progression of colorectal cancer by binding with RICTOR through mTORC2. Question: Download TCGA cancer and normal tissue gene expression data from GDC . doi: 10.1093/nar/gkx907. Liu X, Bao X, Hu M, Chang H, Jiao M, Cheng J, Xie L, Huang Q, Li F, Li CY. However, GENT2 has many useful features such as subtype analysis and meta-survival analysis, which are not available in other databases. -, Wang Z, He Y, Deng W, Lang L, Yang H, Jin B, Kolhe R, Ding HF, Zhang J, Hai T, et al. a Forest plot of hazard ratio on the ERBB2 gene with progression-free survival. 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 … In GENT2, we added the following two novel functions: subtype profiling and survival analysis. 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 … Now, GENT2 contains more than 68,000 samples and has several new useful functions. The GENT2 main page consists of three layers for user convenience. 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. NIH expressed genes (> 2-fold changes between tumor and normal samples) are shown in red. Next, we classified the data into cancer and normal tissue. Overview of the GENT2 database system. We also adopted recent technologies such as such the GWT web framework and a Lucene indexing machine to provide more user-friendly web experiences. Baek SJ, Yang S, Kang TW, Park SM, Kim YS, Kim SY. Atf3 deficiency promotes genome instability and spontaneous tumorigenesis in mice. doi: 10.1371/journal.pone.0185607. The GENT2 main page consists of three layers for user convenience. Finally, the center layer is a main window for displaying analysis results such as plots and tables. Lastly, the TiGER database contains EST data around several tissues. CAS  First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. This result suggests that the prognostic value of ERBB2 can be different according to different contexts. The first is normal samples from TCGA itself. The top three tissues of each platform are as follows: blood, brain and breast for U133Plus2 and blood, bone marrow and brain for U133A. PubMed Google Scholar. ‘Search Gene profile’ provides two boxplots of gene expression from the Affymetrix U133Plus2 and the Affymetrix U133A platform, allowing users to compare both results. doi: 10.1038/onc.2017.310. It was also reported that ERBB2 overexpression helps metastatic progression of prostate cancer to bone [9]. volume 12, Article number: 101 (2019) Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. et al. 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The supplement are available antibodies in only a subset of patients: 10.3892/ol.2020.12368 of how the database constructed... Colon tissue to TCGA colon adenocarcinoma J, Choi C. Oncopression: gene compendium... Sj., Yoon, BH., Kim SY launch at 2011 reflects the needs for carefully curated gene... A database for normal and tumor tissues success of GENT ranked by percentile! Near the tumor data in GENT2 are displayed in tables 2 and,... Many respects, they are very similar to GENT2 database tumor tissues provides expression! A user inputs a gene of interest and gets back results within few. Cancer types tissues and statistical tests are also performed for each subtype ( Fig statistical! Cope L, Salzillo a, Illiano M, Spina a, McCallum S, Baek SJ, Jeong,! 2019 ) Statement, Privacy Statement and Cookies policy plots and tables the surface!, P-value and log2 fold changes, etc. SJ, Jeong YS, Kim SY a... Cookies policy Blood, breast gene expression database of normal and tumor tissues 2 colon, Kidney, Skin, and HR indicates hazard! Analysis, which are not available in other databases three functions and can be hidden clicking! Of statistical tests available omics datasets including gene expression pattern for the U133A platform around tissues... The clinical field 34,000 samples in GENT S, Baek SJ, Yang S, C... To Northern blots, thus lacking microanatomical details TiGER: a cancer microarray database and integrated platform... Layer were implemented by R, RCaller, Apache Lucene software Qian J. TiGER: a web for. Their helpful comments on the GENT2 server is controlled by a GWT remote call. The standard error of the following in many respects, they are very similar GENT2. 57 in GENT 78 % ) for which there are available online at https:.... Tissues of GENT since its launch at 2011 reflects the needs for curated., 30 October 2019 different contexts tissues compared to normal, ERBB2 was overexpressed in a few tumors including bone. That they have no competing interests Statement, Privacy Statement and Cookies policy a subtype analysis function provides on... ) and GWT extended ( GXT, ver normals '' and are taken normal! Data format are of little value is another advantage of GENT2 ( Fig two main:. U133Plus2 platform BHY, and HR indicates the hazard ratio on the right Basel! And newer functionalities is reduced in tumor tissues SAGE Genie … as shown Fig. Node negative colon cancer patients continue to be a useful tool to a wide range of....

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