GEPIA: a Web Server for Cancer and Normal Gene Expression Profiling and Interactive Analyses

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2017 Apr 14

PMID 28407145

Citations 5444

Authors

Zefang Tang

Chenwei Li

Boxi Kang

Ge Gao

Cheng Li

Zemin Zhang

Affiliations

Soon will be listed here.

Abstract

Tremendous amount of RNA sequencing data have been produced by large consortium projects such as TCGA and GTEx, creating new opportunities for data mining and deeper understanding of gene functions. While certain existing web servers are valuable and widely used, many expression analysis functions needed by experimental biologists are still not adequately addressed by these tools. We introduce GEPIA (Gene Expression Profiling Interactive Analysis), a web-based tool to deliver fast and customizable functionalities based on TCGA and GTEx data. GEPIA provides key interactive and customizable functions including differential expression analysis, profiling plotting, correlation analysis, patient survival analysis, similar gene detection and dimensionality reduction analysis. The comprehensive expression analyses with simple clicking through GEPIA greatly facilitate data mining in wide research areas, scientific discussion and the therapeutic discovery process. GEPIA fills in the gap between cancer genomics big data and the delivery of integrated information to end users, thus helping unleash the value of the current data resources. GEPIA is available at http://gepia.cancer-pku.cn/.

Citing Articles

Superior preclinical efficacy of co-treatment with BRG1/BRM and FLT3 inhibitor against AML cells with FLT3 mutations.

Fiskus W, Mill C, Piel J, Collins M, Hentemann M, Cuglievan B Blood Cancer J. 2025; 15(1):40.

PMID: 40089460 DOI: 10.1038/s41408-025-01251-7.

Pathological expression of mitochondrial genome-derived circRNA SCAR/mc-COX2 and its ceRNA network in colorectal cancer: implications for clinical significance.

Nourbakhsh S, Mirzaei S, Mohamadhashem F, Naghizadeh M, Razavi A, Mansoori Y BMC Cancer. 2025; 25(1):466.

PMID: 40082804 PMC: 11907809. DOI: 10.1186/s12885-025-13886-7.

A Comprehensive Analysis Revealing BUB1B as a Potential Prognostic and Immunological Biomarker in Lung Adenocarcinoma.

Hao Z, An F, Zhang W, Zhu X, Meng S, Zhao B Int J Mol Sci. 2025; 26(5).

PMID: 40076684 PMC: 11899737. DOI: 10.3390/ijms26052061.

Spatial Transcriptomics Reveals Novel Mechanisms Involved in Perineural Invasion in Pancreatic Ductal Adenocarcinomas.

Lakis V, Chan N, Lyons R, Blackburn N, Nguyen T, Chang C Cancers (Basel). 2025; 17(5).

PMID: 40075699 PMC: 11899704. DOI: 10.3390/cancers17050852.

H2AJ Is a Direct Androgen Receptor Target Gene That Regulates Androgen-Induced Cellular Senescence and Inhibits Mesenchymal Markers in Prostate Cancer Cells.

Heidari Horestani M, Atri Roozbahani G, Baniahmad A Cancers (Basel). 2025; 17(5).

PMID: 40075640 PMC: 11898987. DOI: 10.3390/cancers17050791.

References

Zhou Y, Luoh S, Zhang Y, Watanabe C, Wu T, Ostland M . Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysis. Cancer Res. 2003; 63(18):5781-4. View

Li L, Chaudhuri A, Chant J, Tang Z . PADGE: analysis of heterogeneous patterns of differential gene expression. Physiol Genomics. 2007; 32(1):154-9. DOI: 10.1152/physiolgenomics.00259.2006. View

Uhlen M, Fagerberg L, Hallstrom B, Lindskog C, Oksvold P, Mardinoglu A . Proteomics. Tissue-based map of the human proteome. Science. 2015; 347(6220):1260419. DOI: 10.1126/science.1260419. View

Plitas G, Konopacki C, Wu K, Bos P, Morrow M, Putintseva E . Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer. Immunity. 2016; 45(5):1122-1134. PMC: 5134901. DOI: 10.1016/j.immuni.2016.10.032. View

Welsh J, Sapinoso L, Su A, Kern S, Wang-Rodriguez J, Moskaluk C . Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res. 2001; 61(16):5974-8. View

. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013; 45(6):580-5. PMC: 4010069. DOI: 10.1038/ng.2653. View

Desany B, Zhang Z . Bioinformatics and cancer target discovery. Drug Discov Today. 2004; 9(18):795-802. DOI: 10.1016/S1359-6446(04)03224-6. View

Weinstein J, Collisson E, Mills G, Mills Shaw K, Ozenberger B, Ellrott K . The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013; 45(10):1113-20. PMC: 3919969. DOI: 10.1038/ng.2764. View

Tomlins S, Rhodes D, Perner S, Dhanasekaran S, Mehra R, Sun X . Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. 2005; 310(5748):644-8. DOI: 10.1126/science.1117679. View

10.

Li B, Li T, Pignon J, Wang B, Wang J, Shukla S . Landscape of tumor-infiltrating T cell repertoire of human cancers. Nat Genet. 2016; 48(7):725-32. PMC: 5298896. DOI: 10.1038/ng.3581. View

11.

Wang Z, Gerstein M, Snyder M . RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2008; 10(1):57-63. PMC: 2949280. DOI: 10.1038/nrg2484. View

12.

Gray D, Jubb A, Hogue D, Dowd P, Kljavin N, Yi S . Maternal embryonic leucine zipper kinase/murine protein serine-threonine kinase 38 is a promising therapeutic target for multiple cancers. Cancer Res. 2005; 65(21):9751-61. DOI: 10.1158/0008-5472.CAN-04-4531. View

13.

Loven J, Orlando D, Sigova A, Lin C, Rahl P, Burge C . Revisiting global gene expression analysis. Cell. 2012; 151(3):476-82. PMC: 3505597. DOI: 10.1016/j.cell.2012.10.012. View

14.

Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen S . 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. 2011; 12(6):R54. PMC: 3218842. DOI: 10.1186/gb-2011-12-6-r54. View

15.

. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 2015; 348(6235):648-60. PMC: 4547484. DOI: 10.1126/science.1262110. View

16.

Petryszak R, Keays M, Tang Y, Fonseca N, Barrera E, Burdett T . Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 2015; 44(D1):D746-52. PMC: 4702781. DOI: 10.1093/nar/gkv1045. View

17.

Welsh J, Zarrinkar P, Sapinoso L, Kern S, Behling C, Monk B . Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci U S A. 2001; 98(3):1176-81. PMC: 14728. DOI: 10.1073/pnas.98.3.1176. View

18.

Tang Z, Li C, Zhang K, Yang M, Hu X . GE-mini: a mobile APP for large-scale gene expression visualization. Bioinformatics. 2017; 33(6):941-943. DOI: 10.1093/bioinformatics/btw775. View