Home LiteratureArticle Details
PMID: 20525248 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

A multilevel data integration resource for breast cancer study.

BMC systems biology ·Vol. 4 ·2010-06-03 ·Pages 76

Mosca E, Alfieri R, Merelli I, Viti F, Calabria A, Milanesi L

Abstract

Breast cancer is one of the most common cancer types. Due to the complexity of this disease, it is important to face its study with an integrated and multilevel approach, from genes, transcripts and proteins to molecular networks, cell populations and tissues. According to the systems biology perspective, the biological functions arise from complex networks: in this context, concepts like molecular pathways, protein-protein interactions (PPIs), mathematical models and ontologies play an important role for dissecting such complexity. In this work we present the Genes-to-Systems Breast Cancer (G2SBC) Database, a resource which integrates data about genes, transcripts and proteins reported in literature as altered in breast cancer cells. Beside the data integration, we provide an ontology based query system and analysis tools related to intracellular pathways, PPIs, protein structure and systems modelling, in order to facilitate the study of breast cancer using a multilevel perspective. The resource is available at the URL http://www.itb.cnr.it/breastcancer. The G2SBC Database represents a systems biology oriented data integration approach devoted to breast cancer. By means of the analysis capabilities provided by the web interface, it is possible to overcome the limits of reductionist resources, enabling predictions that can lead to new experiments.

MeSH Terms
Breast Neoplasms/genetics Databases, Genetic Female Humans Internet Models, Biological Research Design Systems Biology/methods
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Mosca Ettore
Institute for Biomedical Technologies, National Research Council, Segrate (Milan), Italy. ettore.mosca@itb.cnr.it
Alfieri Roberta
Merelli Ivan
Viti Federica
Calabria Andrea
Milanesi Luciano
References (42)
42 references, click to expand
  1. Mechanism of cyclin D1 (CCND1, PRAD1) overexpression in human cancer cells: analysis of allele-specific expression.
    Genes Chromosomes Cancer. 1998 May;22(1):66-71 PMID: 9591636
  2. Gene expression profiles of epithelial cells microscopically isolated from a breast-invasive ductal carcinoma and a nodal metastasis.
    Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18147-52 PMID: 15608061
  3. An ordinary differential equation model for the multistep transformation to cancer.
    J Theor Biol. 2004 Dec 21;231(4):515-24 PMID: 15488528
  4. Identification of functionally related genes using data mining and data integration: a breast cancer case study.
    BMC Bioinformatics. 2009 Oct 15;10 Suppl 12:S8 PMID: 19828084
  5. Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology.
    Methods Mol Biol. 2009;577:67-79 PMID: 19718509
  6. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
    BMC Bioinformatics. 2006 Feb 28;7:97 PMID: 16507094
  7. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72 PMID: 19015125
  8. Lethality and centrality in protein networks.
    Nature. 2001 May 3;411(6833):41-2 PMID: 11333967
  9. An automated method for finding molecular complexes in large protein interaction networks.
    BMC Bioinformatics. 2003 Jan 13;4:2 PMID: 12525261
  10. The UCSC Genome Browser Database: update 2009.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D755-61 PMID: 18996895
  11. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  12. Annotating the human genome with Disease Ontology.
    BMC Genomics. 2009 Jul 07;10 Suppl 1:S6 PMID: 19594883
  13. Gene annotation and pathway mapping in KEGG.
    Methods Mol Biol. 2007;396:71-91 PMID: 18025687
  14. Comparative protein modelling by satisfaction of spatial restraints.
    J Mol Biol. 1993 Dec 5;234(3):779-815 PMID: 8254673
  15. Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study.
    Bioessays. 2006 Feb;28(2):199-210 PMID: 16435295
  16. Activin, inhibin and the human breast.
    Mol Cell Endocrinol. 2004 Oct 15;225(1-2):77-82 PMID: 15451571
  17. The Human Protein Atlas--a tool for pathology.
    J Pathol. 2008 Dec;216(4):387-93 PMID: 18853439
  18. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D588-92 PMID: 18984617
  19. InterPro: the integrative protein signature database.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5 PMID: 18940856
  20. Cyclins and breast cancer.
    J Mammary Gland Biol Neoplasia. 2004 Jan;9(1):95-104 PMID: 15082921
  21. An ontology for cell types.
    Genome Biol. 2005;6(2):R21 PMID: 15693950
  22. The microRNA.org resource: targets and expression.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D149-53 PMID: 18158296
  23. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15 PMID: 18940862
  24. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.
    Neoplasia. 2007 Feb;9(2):166-80 PMID: 17356713
  25. The Stanford Microarray Database: implementation of new analysis tools and open source release of software.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D766-70 PMID: 17182626
  26. Network-based prediction of protein function.
    Mol Syst Biol. 2007;3:88 PMID: 17353930
  27. A rat mammary gland cancer cell with stem cell properties of self-renewal and multi-lineage differentiation.
    Cytotechnology. 2008 Sep;58(1):25-32 PMID: 19034680
  28. Cyclin gene amplification and overexpression in breast and ovarian cancers: evidence for the selection of cyclin D1 in breast and cyclin E in ovarian tumors.
    Int J Cancer. 1996 Aug 22;69(4):247-53 PMID: 8797862
  29. Cancer as a robust system: implications for anticancer therapy.
    Nat Rev Cancer. 2004 Mar;4(3):227-35 PMID: 14993904
  30. A data integration approach for cell cycle analysis oriented to model simulation in systems biology.
    BMC Syst Biol. 2007 Aug 01;1:35 PMID: 17678529
  31. Bifurcation analysis of the regulatory modules of the mammalian G1/S transition.
    Bioinformatics. 2004 Jul 10;20(10):1506-11 PMID: 15231543
  32. The Universal Protein Resource (UniProt) 2009.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D169-74 PMID: 18836194
  33. The cell cycle DB: a systems biology approach to cell cycle analysis.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D641-5 PMID: 18160409
  34. Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man.
    Cell. 2002 Jul 26;110(2):143-51 PMID: 12150923
  35. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D301-3 PMID: 17142228
  36. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
    PLoS Comput Biol. 2009 Jul;5(7):e1000431 PMID: 19578431
  37. The breast cancer information core: database design, structure, and scope.
    Hum Mutat. 2000;16(2):123-31 PMID: 10923033
  38. The hallmarks of cancer.
    Cell. 2000 Jan 7;100(1):57-70 PMID: 10647931
  39. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
    Bioinformatics. 2003 Mar 1;19(4):524-31 PMID: 12611808
  40. Reactome knowledgebase of human biological pathways and processes.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22 PMID: 18981052
  41. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms.
    Bioinformatics. 2003 Jan 22;19(2):270-7 PMID: 12538249
  42. The BioGRID Interaction Database: 2008 update.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40 PMID: 18000002
Article Info
Journal
BMC systems biology
Abbr.
BMC Syst Biol
ISSN
1752-0509
DOI
10.1186/1752-0509-4-76
Email
ettore.mosca@itb.cnr.it
Published
2010-06-03
Epub
2010-00-03
Pages
76
Language
English
Region
England
NLM ID
101301827
PMCID
PMC2900226
Subset
IM
External Links
PubMed source DOI: 10.1186/1752-0509-4-76 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2