Publications
All data generated by The Cancer Genome Atlas (TCGA) Research Network are made open to the public through the Data Coordinating Center and the TCGA Data Portal. The following is a growing list of publications from the TCGA Research Network (designated with an *) and from other investigators who have successfully leveraged the TCGA data for their own work.
Ibragimova, I., Maradeo, M.E., Dulaimi, E. and Cairns, P. (2013) Aberrant promoter hypermethylation of PBRM1, BAP1, SETD2, KDM6A and other chromatin-modifying genes is absent or rare in clear cell RCC. Epigenetics. 8(5):486-493. View PubMed abstract.
Eng, K.H., Wang, S., Bradley, W.H., Rader, J.S. and Kendziorski, C. (2013) Pathway index models for construction of patient-specific risk profiles. Stat Med. 32(9):1524-1535. View PubMed Abstract.
Arimappamagan, A., Somasundaram, K., Thennarasu, K., Peddagangannagari, S., Srinivasan, H., Shailaja, B.C., Samuel, C., Patric, I.R., Shukla, S., Thota, B., et al. (2013) A fourteen gene GBM prognostic signature identifies association of immune response pathway and mesenchymal subtype with high risk group. PLoS One. 8(4):e62042. Read the full article.
Bozdag, S., Li, A., Riddick, G., Kotliarov, Y., Baysan, M., Iwamoto, F.M., Cam, M.C., Kotliarova, S. and Fine, H.A. (2013) Age-specific signatures of glioblastoma at the genomic, genetic, and epigenetic levels. PLoS One. 8(4):e62982. Read the full article.
Kodigepalli, K.M., Anur, P., Spellman, P., Sims, P.J. and Nanjundan, M. (2013) Phospholipid Scramblase 1, an interferon-regulated gene located at 3q23, is regulated by SnoN/SkiL in ovarian cancer cells. Mol Cancer. 12:32. Read the full article.
Safaee, M., Clark, A.J., Oh, M.C., Ivan, M.E., Bloch, O., Kaur, G., Sun, M.Z., Kim, J.M., Oh, T., Berger, M.S., et al. (2013) Overexpression of CD97 confers an invasive phenotype in glioblastoma cells and is associated with decreased survival of glioblastoma patients. PLoS One. 8(4):e62765. Read the full article.
Wan, Y.-W., Mach, C.M., Allen, G., Anderson, M.L. and Liu, Z. (2013) On the reproducibility of TCGA ovarian cancer microRNA profiles. ArXiv. eprint arXiv:1304.6966. View abstract.
Hakimi, A.A., Ostrovnaya, I., Reva, B.A., Schultz, N., Chen, Y.-B., Gonen, M., Liu, H., Takeda, S., Voss, M.H., Tickoo, S.K., et al. (2013) Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA Research Network. Clin Cancer Res. doi: 10.1158/1078-0432.CCR-12-3886. View PubMed abstract.
Joung, J.-G., Kim, D., Kim, K.H. and Kim, J.H. (2013) Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. J Am Med Inform Assoc. doi:10.1136/amiajnl-2012-001571 . View PubMed abstract.
Robbins, D.E., Grüneberg, A., Deus, H.F., Tanik, M.M. and Almeida, J.S. (2013) A self-updating road map of The Cancer Genome Atlas. Bioinformatics. doi: 10.1093/bioinformatics/btt141. Read the full article.
