HCMDB: the Human Cancer Metastasis Database

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2017 Nov 1

PMID 29088455

Citations 81

Authors

Guantao Zheng

Yijie Ma

Yang Zou

An Yin

Wushuang Li

Dong Dong

Affiliations

Soon will be listed here.

Abstract

Metastasis is the main event leading to death in cancer patients. Over the past decade, high-throughput technologies have provided genome-wide view of transcriptomic changes associated with cancer metastases. Many microarray and RNA sequencing studies have addressed metastases-related expression patterns in various types of cancer, and the number of relevant works continues to increase rapidly. These works have characterized genes that orchestrate the metastatic phenotype of cancer cells. However, these expression data have been deposited in various repositories, and efficiently analyzing these data is still difficult because of the lack of an integrated data mining platform. To facilitate the in-depth analyses of transcriptome data on metastasis, it is quite important to make a comprehensive integration of these metastases-related expression data. Here, we presented a database, HCMDB (the human cancer metastasis database, http://hcmdb.i-sanger.com/index), which is freely accessible to the research community query cross-platform transcriptome data on metastases. HCMDB is developed and maintained as a useful resource for building the systems-biology understanding of metastasis.

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References

Weigman V, Chao H, Shabalin A, He X, Parker J, Nordgard S . Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. Breast Cancer Res Treat. 2011; 133(3):865-80. PMC: 3387500. DOI: 10.1007/s10549-011-1846-y. View

Li J, Sun C, Li W, Chao R, Huang C, Zhou X . Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. Nucleic Acids Res. 2015; 44(D1):D944-51. PMC: 4702907. DOI: 10.1093/nar/gkv1282. View

Crea F, Clermont P, Parolia A, Wang Y, Helgason C . The non-coding transcriptome as a dynamic regulator of cancer metastasis. Cancer Metastasis Rev. 2013; 33(1):1-16. PMC: 3988524. DOI: 10.1007/s10555-013-9455-3. View

Kimbung S, Johansson I, Danielsson A, Veerla S, Egyhazi Brage S, Frostvik Stolt M . Transcriptional Profiling of Breast Cancer Metastases Identifies Liver Metastasis-Selective Genes Associated with Adverse Outcome in Luminal A Primary Breast Cancer. Clin Cancer Res. 2015; 22(1):146-57. DOI: 10.1158/1078-0432.CCR-15-0487. View

Lujambio A, Esteller M . How epigenetics can explain human metastasis: a new role for microRNAs. Cell Cycle. 2009; 8(3):377-82. DOI: 10.4161/cc.8.3.7526. View

Poste G, Fidler I . The pathogenesis of cancer metastasis. Nature. 1980; 283(5743):139-46. DOI: 10.1038/283139a0. View

Ramaswamy S, Ross K, Lander E, Golub T . A molecular signature of metastasis in primary solid tumors. Nat Genet. 2002; 33(1):49-54. DOI: 10.1038/ng1060. View

Woelfle U, Cloos J, Sauter G, Riethdorf L, Janicke F, van Diest P . Molecular signature associated with bone marrow micrometastasis in human breast cancer. Cancer Res. 2003; 63(18):5679-84. View

Meyniel J, Cottu P, Decraene C, Stern M, Couturier J, Lebigot I . A genomic and transcriptomic approach for a differential diagnosis between primary and secondary ovarian carcinomas in patients with a previous history of breast cancer. BMC Cancer. 2010; 10:222. PMC: 2891634. DOI: 10.1186/1471-2407-10-222. View

10.

Hanahan D, Weinberg R . The hallmarks of cancer. Cell. 2000; 100(1):57-70. DOI: 10.1016/s0092-8674(00)81683-9. View

11.

Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M . Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5. PMC: 3146043. DOI: 10.1038/nbt.1621. View

12.

Lee J, Park K, Lim S, Kim H, Yoo K, Jung K . Mutational profiling of brain metastasis from breast cancer: matched pair analysis of targeted sequencing between brain metastasis and primary breast cancer. Oncotarget. 2015; 6(41):43731-42. PMC: 4791262. DOI: 10.18632/oncotarget.6192. View

13.

Schell M, Yang M, Missiaglia E, Delorenzi M, Soneson C, Yue B . A Composite Gene Expression Signature Optimizes Prediction of Colorectal Cancer Metastasis and Outcome. Clin Cancer Res. 2015; 22(3):734-45. PMC: 4802496. DOI: 10.1158/1078-0432.CCR-15-0143. View

14.

Seiler R, Lam L, Erho N, Takhar M, Mitra A, Buerki C . Prediction of Lymph Node Metastasis in Patients with Bladder Cancer Using Whole Transcriptome Gene Expression Signatures. J Urol. 2016; 196(4):1036-41. DOI: 10.1016/j.juro.2016.04.061. View

15.

Pizzini S, Bisognin A, Mandruzzato S, Biasiolo M, Facciolli A, Perilli L . Impact of microRNAs on regulatory networks and pathways in human colorectal carcinogenesis and development of metastasis. BMC Genomics. 2013; 14:589. PMC: 3766699. DOI: 10.1186/1471-2164-14-589. View

16.

Jiang C, Li X, Zhao H, Liu H . Long non-coding RNAs: potential new biomarkers for predicting tumor invasion and metastasis. Mol Cancer. 2016; 15(1):62. PMC: 5043609. DOI: 10.1186/s12943-016-0545-z. View

17.

Kimbung S, Kovacs A, Bendahl P, Malmstrom P, Ferno M, Hatschek T . Claudin-2 is an independent negative prognostic factor in breast cancer and specifically predicts early liver recurrences. Mol Oncol. 2013; 8(1):119-28. PMC: 5528500. DOI: 10.1016/j.molonc.2013.10.002. View

18.

Sun J, Chen X, Wang Z, Guo M, Shi H, Wang X . A potential prognostic long non-coding RNA signature to predict metastasis-free survival of breast cancer patients. Sci Rep. 2015; 5:16553. PMC: 4637883. DOI: 10.1038/srep16553. View

19.

Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E . The role of site accessibility in microRNA target recognition. Nat Genet. 2007; 39(10):1278-84. DOI: 10.1038/ng2135. View

20.

Del Rio M, Mollevi C, Vezzio-Vie N, Bibeau F, Ychou M, Martineau P . Specific extracellular matrix remodeling signature of colon hepatic metastases. PLoS One. 2013; 8(9):e74599. PMC: 3762755. DOI: 10.1371/journal.pone.0074599. View