Abstract
Epigenetic modifications affect gene expression and thereby govern a wide range of biological processes such as differentiation, development and tumorigenesis. Recent initiatives to define genome-wide DNA methylation and histone modification profiles by microarray and sequencing methods have led to the construction of databases. These databases are repositories for international epigenetic consortiums or provide mining results from PubMed, but do not integrate the epigenetic information with gene expression changes. In order to overcome this limitation, we constructed EPITRANS, a novel database that visualizes the relationships between gene expression and epigenetic modifications. EPITRANS uses combined analysis of epigenetic modification and gene expression to search for cell function-related epigenetic and transcriptomic alterations (Freely available on the web at http://epitrans.org).
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bird, A. (2007). Perceptions of epigenetics. Nature 447, 396–398.
Chadwick, L.H. (2012). The NIH roadmap epigenomics program data resource. Epigenomics 4, 317–324.
Consortium, T.E.P. (2011). A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9, e1001046.
Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V.K., Attwood, J., Burger, M., Burton, J., Cox, T.V., Davies, R., Down, T.A., et al. (2006). DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378–1385.
Fang, Y.C., Lai, P.T., Dai, H.J., and Hsu, W.L. (2011). MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature. BMC Bioinformatics 12, 471.
Fingerman, I.M., McDaniel, L., Zhang, X., Ratzat, W., Hassan, T., Jiang, Z., Cohen, R.F., and Schuler, G.D. (2011). NCBI Epigenomics: a new public resource for exploring epigenomic data sets. Nucleic Acids Res. 39, D908–912.
Gendler, K., Paulsen, T., and Napoli, C. (2008). ChromDB: the chromatin database. Nucleic Acids Res.36, D298–302.
Grunau, C., Renault, E., Rosenthal, A., and Roizes, G. (2001). MethDB—a public database for DNA methylation data. Nucleic Acids Res. 29, 270–274.
He, X., Chang, S., Zhang, J., Zhao, Q., Xiang, H., Kusonmano, K., Yang, L., Sun, Z.S., Yang, H., and Wang, J. (2008). Methy-Cancer: the database of human DNA methylation and cancer. Nucleic Acids Res. 36, D836–841.
Kondo, Y., Shen, L., and Issa, J.P. (2003). Critical role of histone methylation in tumor suppressor gene silencing in colorectal cancer. Mol. Cell Biol. 23, 206–215.
Krivtsov, A.V., Feng, Z., Lemieux, M.E., Faber, J., Vempati, S., Sinha, A.U., Xia, X., Jesneck, J., Bracken, A.P., Silverman, L.B., et al. (2008). H3K79 methylation profiles define murine and human MLL-AF4 leukemias. Cancer Cell 14, 355–368
Lv, J., Liu, H., Su, J., Wu, X., Li, B., Xiao, X., Wang, F., Wu, Q., and Zhang, Y. (2012). DiseaseMeth: a human disease methylation database. Nucleic Acids Res. 40, D1030–1035.
Meng, C.F., Zhu, X.J., Peng, G., and Dai, D.Q. (2007). Re-expression of methylation-induced tumor suppressor gene silencing is associated with the state of histone modification in gastric cancer cell lines. World J. Gastroenterol. 13, 6166–6171.
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628.
Ongenaert, M., Van Neste, L., De Meyer, T., Menschaert, G., Bekaert, S., and Van Criekinge, W. (2008). PubMeth: a cancer methylation database combining text-mining and expert annotation. Nucleic Acids Res. 36, D842–846.
Smyth, G.K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article3.
Sullivan, S., Sink, D.W., Trout, K.L., Makalowska, I., Taylor, P.M., Baxevanis, A.D., and Landsman, D. (2002). The histone database. Nucleic Acids Res. 30, 341–342.
Xin, Y., Chanrion, B., O’Donnell, A.H., Milekic, M., Costa, R., Ge, Y., and Haghighi, F.G. (2012). MethylomeDB: a database of DNA methylation profiles of the brain. Nucleic Acids Res. 40, D1245–1249.
Zhang, Y., Lv, J., Liu, H., Zhu, J., Su, J., Wu, Q., Qi, Y., Wang, F., and Li, X. (2010). HHMD: the human histone modification database. Nucleic Acids Res. 38, D149–154.
Author information
Authors and Affiliations
Corresponding author
Additional information
These authors contributed equally to this work.
About this article
Cite this article
Cho, S.Y., Chai, J.C., Park, S.J. et al. EPITRANS: A database that integrates epigenome and transcriptome data. Mol Cells 36, 472–475 (2013). https://doi.org/10.1007/s10059-013-0249-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10059-013-0249-9