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      GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis

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          Abstract

          Introduced in 2017, the GEPIA (Gene Expression Profiling Interactive Analysis) web server has been a valuable and highly cited resource for gene expression analysis based on tumor and normal samples from the TCGA and the GTEx databases. Here, we present GEPIA2, an updated and enhanced version to provide insights with higher resolution and more functionalities. Featuring 198 619 isoforms and 84 cancer subtypes, GEPIA2 has extended gene expression quantification from the gene level to the transcript level, and supports analysis of a specific cancer subtype, and comparison between subtypes. In addition, GEPIA2 has adopted new analysis techniques of gene signature quantification inspired by single-cell sequencing studies, and provides customized analysis where users can upload their own RNA-seq data and compare them with TCGA and GTEx samples. We also offer an API for batch process and easy retrieval of the analysis results. The updated web server is publicly accessible at http://gepia2.cancer-pku.cn/.

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          Most cited references 21

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          A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

          When running experiments that involve multiple high density oligonucleotide arrays, it is important to remove sources of variation between arrays of non-biological origin. Normalization is a process for reducing this variation. It is common to see non-linear relations between arrays and the standard normalization provided by Affymetrix does not perform well in these situations. We present three methods of performing normalization at the probe intensity level. These methods are called complete data methods because they make use of data from all arrays in an experiment to form the normalizing relation. These algorithms are compared to two methods that make use of a baseline array: a one number scaling based algorithm and a method that uses a non-linear normalizing relation by comparing the variability and bias of an expression measure. Two publicly available datasets are used to carry out the comparisons. The simplest and quickest complete data method is found to perform favorably. Software implementing all three of the complete data normalization methods is available as part of the R package Affy, which is a part of the Bioconductor project http://www.bioconductor.org. Additional figures may be found at http://www.stat.berkeley.edu/~bolstad/normalize/index.html
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            The Genotype-Tissue Expression (GTEx) project.

            Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
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              Is Open Access

              The Cancer Genome Atlas Pan-Cancer analysis project.

              The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                02 July 2019
                22 May 2019
                22 May 2019
                : 47
                : W1
                : W556-W560
                Affiliations
                [1 ]School of Life Sciences and BIOPIC, Peking University, Beijing 100871, China
                [2 ]Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
                [3 ]Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
                Author notes
                To whom correspondence should be addressed. Tel: +86 10 62768190; Fax: +86 10 62768190; Email: zemin@ 123456pku.edu.cn

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

                This author will join IBM China Research Laboratory (CRL) as a research scientist.

                Article
                gkz430
                10.1093/nar/gkz430
                6602440
                31114875
                © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                Counts
                Pages: 5
                Product
                Funding
                Funded by: Key Technologies R&D Program 10.13039/501100012165
                Award ID: 2016YFC0900100
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 81573022
                Award ID: 31530036
                Award ID: 91742203
                Categories
                Web Server Issue

                Genetics

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