Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Jan;39(Database issue):D889-94.
doi: 10.1093/nar/gkq857. Epub 2010 Sep 28.

DAnCER: disease-annotated chromatin epigenetics resource

Andrei L Turinsky  1 , Brian Turner, Rosanne C Borja, James A Gleeson, Michael Heath, Shuye Pu, Thomas Switzer, Dong Dong, Yunchen Gong, Tuan On, Xuejian Xiong, Andrew Emili, Jack Greenblatt, John Parkinson, Zhaolei Zhang, Shoshana J Wodak
Affiliations

DAnCER: disease-annotated chromatin epigenetics resource

Andrei L Turinsky et al. Nucleic Acids Res. 2011 Jan.

Abstract

Chromatin modification (CM) is a set of epigenetic processes that govern many aspects of DNA replication, transcription and repair. CM is carried out by groups of physically interacting proteins, and their disruption has been linked to a number of complex human diseases. CM remains largely unexplored, however, especially in higher eukaryotes such as human. Here we present the DAnCER resource, which integrates information on genes with CM function from five model organisms, including human. Currently integrated are gene functional annotations, Pfam domain architecture, protein interaction networks and associated human diseases. Additional supporting evidence includes orthology relationships across organisms, membership in protein complexes, and information on protein 3D structure. These data are available for 962 experimentally confirmed and manually curated CM genes and for over 5000 genes with predicted CM function on the basis of orthology and domain composition. DAnCER allows visual explorations of the integrated data and flexible query capabilities using a variety of data filters. In particular, disease information and functional annotations are mapped onto the protein interaction networks, enabling the user to formulate new hypotheses on the function and disease associations of a given gene based on those of its interaction partners. DAnCER is freely available at http://wodaklab.org/dancer/.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Portion of the DAnCER statistics page. Histogram summarizing disease annotations for human CM genes. Bars represent the number of genes in the dataset (vertical axis, logarithmic scale), associated with a given number of distinct disease annotations in OMIM (32) (horizontal axis). Shown are disease associations for genes with a confirmed CM function (blue bars), and disease associations for genes whose CM function has been inferred by computational methods and not yet confirmed (red bars). The majority of genes have only one disease association.
Figure 2.
Figure 2.
Visualization of disease annotations mapped onto the protein interaction neighborhood in DAnCER. The graph illustrates the interaction neighborhood of a human histone methyltransferase SUV420H2 (node highlighted in yellow), which interacts with three proteins from the RB1 family: Rb1 (retinoblastoma 1), RBL1 (retinoblastoma-like 1) and RBL2 (retinoblastoma-like 2). Although OMIM does not provide a direct disease association for SUV420H2, its interactor Rb1 is implicated in four different types of tumors (dark red parallelograms). The domain composition for all proteins is also shown (orange triangles), indicating that all RB1-family proteins except RBL2 share the same combination of domains; whereas SUV420H2 contains a SET domain, which is associated with lysine methyltransferase enzymes. The labels on the protein-interaction edges indicate that each interaction is supported by one experimental study (51). The node sizes are proportional to the node degrees, indicating that the RB1-family proteins have many more interactors (shown after double-clicking on the node). Similarly, bladder cancer and osteosarcoma are associated with more genes than retinoblastoma and pinealoma; and SET domain occurs in more human proteins than any of the other four domains shown. Views are generated with Cytoscape Web (36).
See this image and copyright information in PMC

Similar articles

  • BioGRID: a general repository for interaction datasets.
    Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Stark C, et al. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9. doi: 10.1093/nar/gkj109. Nucleic Acids Res. 2006. PMID: 16381927 Free PMC article.
  • Genome-wide prediction of C. elegans genetic interactions.
    Zhong W, Sternberg PW. Zhong W, et al. Science. 2006 Mar 10;311(5766):1481-4. doi: 10.1126/science.1123287. Science. 2006. PMID: 16527984
  • The BioGRID Interaction Database: 2008 update.
    Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M. Breitkreutz BJ, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40. doi: 10.1093/nar/gkm1001. Epub 2007 Nov 13. Nucleic Acids Res. 2008. PMID: 18000002 Free PMC article.
  • Lessons from modENCODE.
    Brown JB, Celniker SE. Brown JB, et al. Annu Rev Genomics Hum Genet. 2015;16:31-53. doi: 10.1146/annurev-genom-090413-025448. Epub 2015 Jun 26. Annu Rev Genomics Hum Genet. 2015. PMID: 26133010 Review.
  • Genetics of eukaryotic RNA polymerases I, II, and III.
    Archambault J, Friesen JD. Archambault J, et al. Microbiol Rev. 1993 Sep;57(3):703-24. doi: 10.1128/mr.57.3.703-724.1993. Microbiol Rev. 1993. PMID: 8246845 Free PMC article. Review.
See all similar articles

Cited by

See all "Cited by" articles

References

    1. Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell. 2007;128:707–719. - PubMed
    1. Groth A, Rocha W, Verreault A, Almouzni G. Chromatin challenges during DNA replication and repair. Cell. 2007;128:721–733. - PubMed
    1. Minucci S, Pelicci PG. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat. Rev. Cancer. 2006;6:38–51. - PubMed
    1. Feinberg AP. Phenotypic plasticity and the epigenetics of human disease. Nature. 2007;447:433–440. - PubMed
    1. Kouzarides T. Chromatin modifications and their function. Cell. 2007;128:693–705. - PubMed

Publication types