The source for each Fact is indicated by the following icons: double gold stars, primary Fact from a full text paper; single gold star, primary fact from an abstract; red dot, `secondary' Fact (i.e. Finally, BCGD and other similar databases can be used as a platform for the deposition of primary unpublished data in much the same way that DNA sequence is frequently entered directly into Genbank in the absence of conventional publication. Genes containing genetic variants associated with an increased risk of developing breast cancer were identified using gene names and corresponding gene symbols. This strategy is: (((((((``ONCOGENE'' [TEXT WORD] OR ``ONCOGENES'' [MESH TERMS]) OR ``GENES, SUPPRESSOR, TUMOR'' [MESH TERMS]) OR ``PROTO-ONCOGENE PROTEINS'' [MESH TERMS]) OR ``PROTEIN-TYROSINE KINASE'' [MESH TERMS]) OR ``NEOPLASMS'' [MESH TERMS]) OR ``NEOPLASM PROTEINS'' [MESH TERMS]) OR ``DNA, NEOPLASM'' [MESH TERMS]) OR ``TUMOR MARKERS, BIOLOGICAL'' [MESH TERMS]). Most of these facts were obtained from PubMed abstracts, but 180 of them were obtained from the complete paper and thus represent facts that are not necessarily present in PubMed. 1American Cancer Society. 2Wood WC, Muss HB, Solin LJ, Olopade OL: Malignant Tumors of the Breast. As others have pointed out, there is no single "mutated gene sequence responsible for breast cancer". A significant effort was made to include within BCGD as complete a synonym table as possible, allowing a user to query the database and retrieve all relevant facts using any one of the gene names. The Breast Cancer Gene Database (BCGD) is a compendium of molecular genetic data relating to genes involved in breast cancer, and which is freely available via the World Wide Web. This site is best viewed with Chrome, Edge, or Firefox. This approach has the added benefit of providing a natural way to divide references among curators and to make the task of extracting data from these publications more manageable. Genes that increase the risk of breast cancer are BRCA1 and BRCA2. Data in BCGD is linked to other on-line resources such as Entrez, GeneCards and On-Line Mendelian Inheritance in Man. Ohkawa H, Ostell J and Bryant S. . The GENT2 database provides the following five functions: 1) a landscape of gene expression profile across 72 normal and tumor tissues, 2) cancer subtype profiling, 3) statistical significance of gene expression difference between normal and tumor samples, 4) a prognostic value of gene expression, and 5) meta-survival analysis (Fig. By identifying the genes which are breast cancer genes, by identifying the synonyms by which each gene is known, by collecting all the information about each gene in one place, and by organizing it by topic, BCGD's curators make information available that is practically inaccessible in PubMed. Complementary & Alternative Medicine (CAM), Coping with Your Feelings During Advanced Cancer, Emotional Support for Young People with Cancer, Young People Facing End-of-Life Care Decisions, Late Effects of Childhood Cancer Treatment, Tech Transfer & Small Business Partnerships, Frederick National Laboratory for Cancer Research, Milestones in Cancer Research and Discovery, Step 1: Application Development & Submission, expanded study with focus on ductal versus lobular subtypes, U.S. Department of Health and Human Services. 27: 18–24. McGraw Hill, Inc pp. All words in the Fact and Comment fields of the database can be searched by Keyword. View Dataset. A wide variety of such resources are available to the breast cancer gene research community, ranging from repositories of primary data (e.g. The function of the BRCA genes is to repair cell damage and keep breast, ovarian, and other cells growing normally. Because the facts in BCGD are extracted from the published literature, it is important to begin by identifying breast cancer gene publications. BCGD curators used a combination of traditional browsing techniques and the PubMed search described above to identify publications from which to extract facts. 1995 Ismb 3: 259–267. Internet Explorer). It is shown here that, at the current rate, one would need to scan in excess of 130 journals and read in excess of 27 papers a day to keep up with the field of Breast Cancer Genes, and the rate of accumulation of literature in this field is still increasing. Citations and their abstracts identified by searching PubMed are automatically imported into BCGD and presented to the curators as an alphabetical list with the titles of articles as links to data entry forms. What is the KM plotter? Breast cancer is the most frequent tumor in women. volume 18, pages7958–7965(1999)Cite this article. 27: 49–54. Facts are brief statements of findings, limited to 80 characters. A link provides access to Facts previously entered by any of the curators so that duplicate entries can be avoided. 1999 Nucleic Acids Res. Unless augmented with further evidence for oncogenicity, genes that only manifest aberrant regulation in breast neoplasms are not included in the database. The goal of the Breast Cancer Gene Database is to contain a complete description of all of the genes which identified as tumor genes involved in breast cancer. Data is deposited and retrieved from the database through a set of interactive Web forms, making it both platform-independent and universally accessible in facilitating worldwide collaborative authoring of the database. Data show that the engineered B cells expressing Bcl-x(L) exhibited progressively lower increases in apoptosis activation. The database fact listing for BRCA1 under the Topic `Cell location' variously lists the cytoplasm and secretory vesicles as well as the nucleus (not shown). The data … Oncogene 18, 7958–7965 (1999). A detailed description of the software package used by the Tumor Gene Database is being published elsewhere (DL Steffen, AE Levine, S Yarus, RA Baasiri and DA Wheeler Digital Reviews in Molecular Biology: A Model for Structured Digital Publication (2000). Presented this way, the viewer readily acquires a sense for the reproducibility of the given fact. Development of a sensitive and selective search strategy for PubMed citations relevant to tumor genes has been a significant effort, is ongoing, and will be described more fully elsewhere. Using the G9a-suppressed gene signature, … In the case of permitted digital reproduction, please credit the National Cancer Institute as the source and link to the original NCI product using the original product's title; e.g., “TCGA's Study of Breast Ductal Carcinoma was originally published by the National Cancer Institute.”. In other words, a keyword search with `receptor kinase' will find all entries with either `receptor' or `kinase' in the fact or comment fields. In addition, this site contains a number of reviews, some of which overlap in content with BCGD. 103–107. This information is derived from FDA labels, NCCN and other professional society guidelines, clinical trials, peer-reviewed publications, and more. the cited paper mentions the fact but cites one of its references as the source of that fact) from a full paper; blue dot, secondary Fact from an abstract; red star, primary fact from a Review; blue star, secondary fact from a review; no symbol, source unknown (e.g. The breast cancer database is a publicly available dataset from the UCI Machine learning Repository. Rebhan M, Chalifa-Caspi V, Prilusky J and Lancet D. . My Cancer Genome contains information on the clinical impact of molecular biomarkers in cancer-related genes, proteins, and other biomarker types on the use of anticancer therapies in cancer. Number of PubMed citations about breast cancer genes. Street, and O.L. BCGD can be searched either by gene name or keyword. There is very little overlap between BCGD and CGAP; both are important to breast cancer researchers. Future versions of the database should provide direct links to other appropriate biological resources such as GenBank, 3-Dimensional protein or DNA structure Databases mainly NCBI's Molecular Modeling Database (Ohkawa et al., 1995), and the Mouse Genome Database (Blake et al., 1999). LocusLink (http://www.ncbi.nlm.nih.gov/LocusLink/); GeneCards (Rebhan et al., 1998), and HUGO (http://ash.gene.ucl.ac.uk/nomenclature/) are extremely useful resources that are similar one to another. No effort is made to resolve such conflicts, but rather they are left in for the viewer to judge. The PubMed database (http://www.ncbi.nlm.nih.gov/Entrez/medline.html) was searched for citations to these publications. The Web-based data entry interface allows data to be entered into BCGD from anywhere in the world. (In this and the next three figures, the browser's (Netscape's) navigation tools have been hidden). The Breast Cancer Gene Database (BCGD) is a compendium of molecular genetic data relating to genes involved in breast cancer, and which is freely available via the World Wide Web. The current best strategy for identification of all such publications, referred to as the `high stringency search', is: ((((``ONCOGENE'' [TEXT WORD] OR ``ONCOGENES'' [MESH TERMS]) OR ``GENES, SUPPRESSOR, TUMOR'' [MESH TERMS]) OR ``PROTO-ONCOGENE PROTEINS'' [MESH TERMS]) OR ``PROTEIN-TYROSINE KINASE'' [MESH TERMS]), Approximately 95% of the references retrieved by this search are relevant to tumor genes and it retrieves approximately 50% of the relevant references in PubMed. OncoLink (Buhle et al., 1994)). This work was supported by National Cancer Institute grant, CA 70532, awarded as part of the National Action Plan on Breast Cancer. Atlanta: American Cancer Society, Inc. 2010. 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