breast cancer gene database

BCGD currently contains approximately 2270 facts from 1162 publications describing 60 genes identified as breast cancer genes. We detected you are using Internet Explorer. The specimen showed histologically typical small cells with classic neuroendocrine features. Upon review, such a fact can be flagged as `reject', `revise' or `publish'; only facts marked `publish' are available to appear in a search result. This site is best viewed with Chrome, Edge, or Firefox. One of the serious impediments to achieving clinical benefits from this information however, is finding and assessing the significance of mutations … Invasive ductal carcinoma is the most common type of breast cancer. It gives information on tumor features such as tumor size, density, and texture. Described in Results.) The PubMed database (http://www.ncbi.nlm.nih.gov/Entrez/medline.html) was searched for citations to these publications. This information is derived from FDA labels, NCCN and other professional society guidelines, clinical trials, peer-reviewed publications, and more. BCGD is a view into the Tumor Gene Database (http://mbcr.bcm.tmc.edu/ermb/tgdb/tgdb.html) and thus uses exactly the same software and database. It contains several infos base by base, amino acid by amino acid on the breast cancer genes coding sequence. The Breast Cancer Gene Database: a collaborative information resource. Philadelphia, Pa: Lippincott Williams & Wilkins; 2005: 1420. This initial search misses many references which concern a Breast Cancer Gene, but which report results which themselves are not particular to Breast Cancer. BCGD is located at http://mbcr.bcm.tmc.edu/ermb/bcgd/bcgd.html. BCGD's organization by topic affords quick and convenient access to specific pieces of information. The Web-based data entry interface allows data to be entered into BCGD from anywhere in the world. The data in BCGD is extracted from the published biomedical research literature and stored as a collection of `Facts', which in turn are collected into topical categories organized by gene. Every fact in the database is linked to a journal citation. Gene expression profiling is a technique used in molecular biology to query … 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). Barker WC, Garavelli JS, McGarvey PB, Marzec CR, Orcutt BC, Srinivasarao GY, Yeh LS, Ledley RS, Mewes HW, Pfeiffer F, Tsugita A and Wu C. . Most inherited cases of breast cancer are associated with mutations in two genes: BRCA1 (BReast CAncer gene one) and BRCA2 (BReast CAncer gene two).Everyone has BRCA1 and BRCA2 genes. When this strategy was applied, citations to 90 373 publications were identified. Currently, the database contains a reasonably comprehensive list of the genes which have been shown with some certainty to be important in Breast Cancer, the various names given to each of these genes, and a useful collection of basic facts about these genes; subcellular location, size, biochemical activity, and so forth. The breast cancer database is a publicly available dataset from the UCI Machine learning Repository. 2Wood WC, Muss HB, Solin LJ, Olopade OL: Malignant Tumors of the Breast. There are plans to create a prostate and colon-specific extensions of TGDB as well. Indeed, worldwide, breast cancer accounts for almost 23% of all cancers (ex- On the other hand, assessing the performance of proposed biomarkers in different populations or evaluating competing … This work was supported by National Cancer Institute grant, CA 70532, awarded as part of the National Action Plan on Breast Cancer. It comprises about 65–85% of all breast cancer and develops in the milk ducts of the breast. The data … BCGD is a `gene database' in that only the information pertaining to breast cancer and attributable to the characteristics or action of a particular gene is included in the database. Breast cancer cell line MDA-MB-453 response to DHT Species: human … Currently, searches with multiple keywords are treated as a logical `OR'. In addition, data extracted from papers rather than abstracts will frequently be absent from its PubMed citation. 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. McGraw Hill, Inc pp. In: DeVita VT Jr, Hellman S, Rosenberg SA ed. Department of Cell Biology, Baylor College of Medicine, Houston, 77030, Texas, TX, USA, Rudeina A Baasiri, Stanley R Glasser & David A Wheeler, Biomedical Computing, Inc., Houston, 77005, Texas, TX, USA, You can also search for this author in 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. A Keyword search can be limited in scope to either the Fact or Comment field, or it can be limited to only certain Topics in order to increase the specificity of the search result. What have TCGA researchers learned about breast cancer? If you would like to reproduce some or all of this content, see Reuse of NCI Information for guidance about copyright and permissions. Thank you for visiting nature.com. 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. 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. 1). Cancer Facts and Figures 2010. Basal-like subtype shares many genetic features with high-grade serous ovarian cancer, suggesting that the cancers have a common … Atlanta: American Cancer Society, Inc. 2010. Published, Pending, On Hold. Data entry screen for BCGD. The function of the BRCA genes is to repair cell damage and keep breast, ovarian, and other cells growing normally. (2020), Breast Cancer Research and Treatment The following sections present … Data used: Kaggle-Breast Cancer Prediction … ISSN 1476-5594 (online), The Breast Cancer Gene Database: a collaborative information resource, http://mbcr.bcm.tmc.edu/ermb/bcgd/bcgd.html, http://www.ncbi.nlm.nih.gov/Entrez/medline.html, http://www.ncbi.nlm.nih.gov/PubMed/overview.html, http://mbcr.bcm.tmc.edu/ermb/authors.html, http://www.nhgri.nih.gov/ Intramural_research/ Lab_transfer/Bic/, http://mbcr.bcm.tmc.edu/ermb/tgdb/tgdb.html, Exploring the potential microRNA sponge interactions of breast cancer based on some known interactions, High-Precision Biomedical Relation Extraction for Reducing Human Curation Efforts in Industrial Applications, MOBCdb: a comprehensive database integrating multi-omics data on breast cancer for precision medicine, Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer, Identifying miRNA sponge modules using biclustering and regulatory scores. Men can also have breast cancer, although male breast cancer is rare. The relevance between RRM2 level and clinical parameters as well as survival data in breast cancer was analyzed using the Kaplan-Meier Plotter, PrognoScan, and Breast Cancer Gene-Expression Miner (bc-GenExMiner) databases. You are using a browser version with limited support for CSS. Effective treatments include surgery, chemotherapy, radiotherapy, endocrinotherapy and molecular-targeted therapy. The international study tested 34 potential risk genes from 60,466 breast cancer cases worldwide and 53,461 control patients who did not have breast cancer. Correspondence to OncoLink (Buhle et al., 1994)). Similarly, the Breast Cancer Information Core (BIC, http://www.nhgri.nih.gov/ Intramural_research/ Lab_transfer/Bic/) is a specialized database of published and unpublished data on germline mutations in a few breast cancer genes and has little overlap with BCGD. BCGD is an extension of a larger, earlier database called the Tumor Gene Database (http://mbcr.bcm.tmc.edu/ermb/tgdb/tgdb.html) which covers approximately 350 tumor genes. Additional information on breast cancer. TGDB is structured to allow sharing of information among the databases in cases where a given gene can be involved in more than one type of cancer (the majority of cases). It is widely appreciated that the biomedical research literature accumulates at a rate far surpassing that at which anyone can read it, let alone assimilate it. The result of a keyword search organizes Facts first by Gene Name, and then by Topic within a gene. (In this and the next three figures, the browser's (Netscape's) navigation tools have been hidden). Bioinformatics, SUBMITTED). Because the facts in BCGD are extracted from the published literature, it is important to begin by identifying breast cancer gene publications. Despite the fact that it is heavily based on PubMed, a researcher would not be able to extract the information in BCGD from PubMed without duplicating the many hours of work performed by BCGD curators. Thus, the BCGD paradigm has the potential to benefit research into other forms of cancer and will help researchers working on different cancers to effectively share their results. No effort is made to resolve such conflicts, but rather they are left in for the viewer to judge. The BReast CAncer genes database is built for world-wide use. i cation of breast cancer types that is implied by the e ectiveness of the Oncotype DX and PAM50 gene sets. because the gene name rasH matches the medically common word rash. The Kaplan Meier plotter is capable to assess the effect of 54k genes (mRNA, miRNA, protein) on survival in 21 cancer types including breast (n=6,234), ovarian (n=2,190), lung (n=3,452), and gastric (n=1,440) cancer.Sources for the databases include GEO, EGA, and TCGA. Tateno Y and Gojobori T. . 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. 1999 Nucleic Acids Res. More recently, digital resources have provided additional solutions to this problem. For some of these names, a large number of irrelevant citations are retrieved, e.g. volume 18, pages7958–7965(1999)Cite this article. Entrez Gene: 672: PubMed articles: BRCA1: OMIM - Gene: 113705: OMIM - Diseases: BROVCA-1 (cancer, breast-ovarian, familial, susceptibility to, type 1 (BROVCA-1)) PNCA-4 (cancer, pancreatic, susceptibility to, type 4 (PNCA-4)) cancer, breast, familial: HGMD: BRCA1: GeneCards: BRCA1: GeneTests: BRCA1: Orphanet: BRCA1 "breast cancer") to get started.Then, click on the tab that says "OMIM dbSNP" to limit results to those loci with a known SNP. --Clinical pathologist, Karolinska University Hospital If one does not know all possible synonyms for a gene, it is very difficult to retrieve all papers pertaining to the gene. After a Fact is entered, the curator may elect to enter another Fact from the same paper, go on to the next paper, or return to a list of all available papers. 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. Individual facts are listed below, organized by Topic. There is very little overlap between BCGD and CGAP; both are important to breast cancer researchers. 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]). The fact may be taken from a primary research paper, from the PubMed abstract of a primary research paper, or from a review. Thereafter, facts about individual genes are searched for by name using the search: GeneName [WORD], This search needs to be repeated for each of the names by which the gene is known (e.g. The cancer can be categorized into four molecular subtypes: HER2-enriched, Luminal A, Luminal B, and Basal-like. The individual Facts originate from a variety of sources. Primary purpose of the tool is a meta-analysis based discovery and validation … Traditionally, this has included books and review articles which summarize a large volume of primary literature. Biology of the Mammary Gland (http://mammary.nih.gov/) is a website that collects a variety of kinds of information of interest to mammary gland researchers, much of which will be valuable to breast cancer researchers. These represent more or less traditional reviews and as such are selective rather than comprehensive and are intended primarily to educate rather than being compendia of data. Equally, an example of an important disease entity which does not significantly … Ohkawa H, Ostell J and Bryant S. . 1999 Nucleic Acids Res. An ENIGMA member is currently defined as a researcher or … To obtain Basal-like subtype shares many genetic features with high-grade serous ovarian cancer, suggesting that the cancers have a common molecular origin and may share therapeutic opportunities, such as: A drug that inhibits blood vessel growth, cutting off the blood supply to the tumor. 25: 14–17. This cancer develops in the breast milk-producing lobules or glands. 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. GOBO is aimed at providing an online tool for prognostic validation of single genes, sets of genes or simple predictors in a pooled breast cancer data set comprising 1881 cases from eleven public data sets analyzed using Affymetrix U133A arrays. The primary report for the fact might be the cited paper, or the cited paper might report the fact as coming from one of its references. What have TCGA researchers learned about breast cancer? Presented this way, the viewer readily acquires a sense for the reproducibility of the given fact. For this application, the editorial functions built in to the system could be used to ensure adequate peer review of information published this way. Mangasarian. Cancer Letters 77 (1994) 163-171. Thus, this initial search is used primarily to develop and maintain the list of Breast Cancer genes. (An analogous comparison is between a dictionary and a book containing the same words and definitions in random order). 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. Data-driven approaches designed to generate models for risk stratification of breast cancer patients have largely uncovered proliferation-related genes which, while they are indisputably effective predictors of survival, do not provide additional insight into the biology underlying their expression . Medical literature: W.H. In addition, the curator can indicate the source of the fact (see the legend to Figure 3) and the status of the fact (e.g. The cancer can be categorized into four molecular subtypes: HER2-enriched, Luminal A, Luminal B, and Basal-like. 88: 1801–1803. BCGD can be searched either by gene name or keyword. The Gene name is listed at the top of the page along with relevant synonyms. A listing of all genes in the database and their synonyms is given in Table 1. It offers the possibility to explore gene-expression of genes of interest in breast cancer. PubMed Google Scholar. Further, The mechanisms for collaborative curation of a gene or set of genes by researchers throughout the world, the mechanisms for editorial oversight by experts in the field (capabilities unique among biological databases of this type) will facilitate its maintenance. Data in BCGD is linked to other on-line resources such as Entrez, GeneCards and On-Line Mendelian Inheritance in Man. To that end, BCGD is structured to accommodate future development. 1999 Nucleic Acids Res. Proto-oncogenes and tumor suppressor genes are included in BCGD if they demonstrate one or more of the following (1) breast cancer-specific activation of transforming activity, e.g. Given the wide variety of traditional and digital resources available to the breast cancer researcher, what additional benefits can be derived from BCGD? On a higher level, breast cancer datasets collected by different institutions can be considered as resamplings from the underlying breast cancer population. Breast Cancer Information Core An Open Access On-Line Breast Cancer Mutation Data Base. This generates a list of genes mostly consisting of and containing most of the breast cancer genes that are transcription factors. GOBO is a user-friendly online tool that allows rapid assessment of gene expression levels, identification of co-expressed genes and association with outcome for single genes, gene sets or gene signatures in an 1881-sample breast cancer data set. Number of PubMed citations about breast cancer genes. It is more of a research project than an information resource. Finally, the World Wide Web (Web)-based interface for adding information and its collaborative capabilities will facilitate BCGD maintenance so that its value to the breast cancer gene community can remain high. If you're looking for SNPs that increase susceptibility to the disease, a good starting point is OMIM.You can search with a simple term (e.g. BCGD offers both short and long term benefits to the breast cancer gene research community. 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. 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 organization facilitates quick searches and rapid retrievals of specific data such as gene characteristics, functions and role in oncogenesis, and is an important factor allowing for continuous updates. 1997 Nucleic Acids Res. The total number of PubMed citations was determined by accumulating the `low stringency' tumor gene references found for each gene for each year between 1989 and 1998 by performing 10 searches where each search contained the term ####[PDAT], where #### is a number between 1989 and 1998, combined with the rest of the search using the AND Boolean operator. 7th ed. This list of genes is not a reliable list of breast cancer genes (nor was it intended by the developers of OMIM to be) and the data in the records for the breast cancer genes (which for the most part are in OMIM) focus more on human genetic disease than on cancer, and may or may not contain information critical to the breast cancer gene researcher; whether a gene encodes a tyrosine kinase, a receptor, or a transcription factor, for example. Cancer Inst. An important tool towards reaching that goal is a strategy for identifying all of the papers published on these genes. (2018), BMC Bioinformatics The result of this search will be a list of genes which is a good approximation of all transcription factors (Figure 4). OMIM is the resource that probably has greater overlap with BCGD than any other. A link provides access to Facts previously entered by any of the curators so that duplicate entries can be avoided.

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