Given the wide variety of traditional and digital resources available to the breast cancer researcher, what additional benefits can be derived from BCGD? 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. Facts pertaining to Cell Location and Cell Type Distribution are visible in this figure. BCGD offers both short and long term benefits to the breast cancer gene research community. This example shows the result of a search for the keyword `Transcription' in the Fact or Comment fields limited to the Topic `Biochemical Type'. In 2010, 207,090 women were estimated to have been diagnosed with invasive breast cancer in the United States and approximately 40,000 women were estimated to have died of their disease.1. Want to use this content on your website or other digital platform? "breast cancer") to get started.Then, click on the tab that says "OMIM dbSNP" to limit results to those loci with a known SNP. 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. 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. bc-GenExMiner v4.5 is a statistical mining tool of published annotated breast cancer transcriptomic data (DNA microarrays [n = 10 716] and RNA-seq [n = 4 712]). Goal: To create a classification model that looks at predicts if the cancer diagnosis is benign or malignant based on several features. --Clinical pathologist, Karolinska University Hospital Each Fact entry includes a brief statement of the fact (bold face lettering), longer comments explicating the Fact where required, a link to the reference for the Fact and the curator's initials in square brackets. 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 . In other words, Facts about p53 entered into the database by a curator interested in, for example, prostate cancer, will be visible to a user searching BCGD for p53 Facts, since the gene is common to both cancers. 1996 J. Natl. Result of a keyword search using receptor as the query term. 1). Bairoch A and Apweiler R. . Wolberg, W.N. Within each topic, information is presented as a list of `facts' plus an optional comment (when pertinent) along with the citation for the fact. Basal-like subtype shares many genetic features with high-grade serous ovarian cancer, suggesting that the cancers have a common … 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. 1999 Nucleic Acids Res. Curators for BCGD and other tumor gene databases are actively being recruited; contact information is available at http://mbcr.bcm.tmc.edu/ermb/authors.html. Number of PubMed citations about breast cancer genes. BCGD curators used a combination of traditional browsing techniques and the PubMed search described above to identify publications from which to extract facts. This site is best viewed with Chrome, Edge, or Firefox. 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.”. 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. 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. BCGD currently contains approximately 2270 facts from 1162 publications describing 60 genes identified as breast cancer genes. 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. With the development of molecular biology, immunology and pharmacogenomics, an increasing amount … If a particular fact is found to be erroneously entered (even after it has been reviewed and published) the curator of that fact can alter it as required. 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. The result of this search will be a list of genes which is a good approximation of all transcription factors (Figure 4). Described here is the Breast Cancer Gene Database (BCGD), an additional resource with unique benefits for breast cancer researchers. In 2010, 1,970 American men were estimated to have been diagnosed and 390 were estimated to have died of breast cancer.1 Due to early detection through use of mammograms and improvements in treatment, breast cancer deaths have steadily decreased since the 1990s. 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. Machine learning techniques to diagnose breast cancer from fine-needle aspirates. The fact may be taken from a primary research paper, from the PubMed abstract of a primary research paper, or from a review. This work was supported by National Cancer Institute grant, CA 70532, awarded as part of the National Action Plan on Breast Cancer. The specimen showed histologically typical small cells with classic neuroendocrine features. This initial search misses many references which concern a Breast Cancer Gene, but which report results which themselves are not particular to Breast Cancer. A listing of all genes in the database and their synonyms is given in Table 1. It is searchable in two ways; by gene name or by keyword. Oncogene 18, 7958–7965 (1999). The PubMed database (http://www.ncbi.nlm.nih.gov/Entrez/medline.html) was searched for citations to these publications. The feasibility of data entry has been demonstrated from multiple sites within the US and the Middle East. Moreover, GOBO offers the possibility of investigation of gene expression levels in breast cancer subgroups and breast cancer cell lines for gene … Medical literature: W.H. What have TCGA researchers learned about breast cancer? 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. 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 cancer can be categorized into four molecular subtypes: HER2-enriched, Luminal A, Luminal B, and Basal-like. If you would like to reproduce some or all of this content, see Reuse of NCI Information for guidance about copyright and permissions. An important tool towards reaching that goal is a strategy for identifying all of the papers published on these genes. Cancer is a category of disease characterized by uncontrolled cell growth and proliferation. 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. Additional information on breast cancer. TCGA's original breast cancer study and expanded study with focus on ductal versus lobular subtypes, Find NCI-supported breast cancer clinical trials. Cancer Letters 77 (1994) 163-171. 27: 95–98. PubMed Google Scholar. We know about several gene faults that can increase breast cancer risk and there are tests for some of them. Information in the database consists of collections of Facts organized by Topic. This information is derived from FDA labels, NCCN and other professional society guidelines, clinical trials, peer-reviewed publications, and more. Information retrieved by a search using a gene name is organized into topical categories, e.g., gene regulation, DNA structure, protein size, function, etc (Figure 3). Currently, BCGD supports hypertext links to OMIM and PubMed. Published, Pending, On Hold. 1994 Proceedings–Eighteenth Annual Symposium on Computer Applications in Medical Care. 103–107. Breast cancer diagnosis and prognosis via linear programming. It gives information on tumor features such as tumor size, density, and texture. Correspondence to 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). Using the `high stringency search', described above, has the disadvantage of eliminating half the relevant citations. 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. In summary, BCGD provides a resource of unique value to the breast cancer researcher with minimal overlap with other existing resources. (2020), Breast Cancer Research and Treatment . 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. The cancer can be categorized into four molecular subtypes: HER2-enriched, Luminal A, Luminal B, and Basal-like. Benson DA, Boguski MS, Lipman DJ, Ostell J, Ouellette BF, Rapp BA and Wheeler DL. Breast cancer is the most frequently diagnosed cancer and the second cause of cancer deaths in women. For example, one could search with the keyword `transcription' and limit the search to the `Biochemical type'. 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. an older fact). Data used: Kaggle-Breast Cancer Prediction … We detected you are using Internet Explorer. Neither of them provide a list of breast cancer genes nor are they intended to provide the breadth and depth of information being collected in BCGD. 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. In the long-term, maximizing the rate of scientific progress will require continuing improvement in the methods for disseminating and retrieving results obtained. The number of references retrieved from PubMed for each of the genes in BCGD is given in Table 1. Traditionally, this has included books and review articles which summarize a large volume of primary literature. All literature references in the database are hypertext links into PubMed and the query gene name appearing at the top of the page is a link into Online Mendelian Inheritance in Man (OMIM, http://www.ncbi.nlm.nih.gov/omim/). Men can also have breast cancer, although male breast cancer is rare. 1997 Nucleic Acids Res. This generates a list of genes mostly consisting of and containing most of the breast cancer genes that are transcription factors. 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. Unless augmented with further evidence for oncogenicity, genes that only manifest aberrant regulation in breast neoplasms are not included in the database. determining the clinical significance of sequence variants in BRCA1, BRCA2 and other known or suspected breast cancer genes, to provide this expert opinion to global database and classification initiatives, and ; to explore optimal avenues of communication of such information at the provider and patient level. Thus, in a practical sense, these also overlap little with BCGD. 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). mechanism of proapoptotic BH3 proteins Bad and Bid binding to Bcl-XL and Bcl-2 in breast cancer cells; a cis-regulatory element in exon 3 that affects splicing of exon 2 in the Bcl-x gene was identified. About 10% of all cases of advanced breast cancer2 are invasive lobular breast carcinoma. Kuska B. . Data show that the engineered B cells expressing Bcl-x(L) exhibited progressively lower increases in apoptosis activation. Over the next dozen years, TCGA generated over 2.5 petabytes of genomic, epigenomic, transcriptomic, and proteomic data. Although, as is discussed below, many Facts are duplicated, providing a complete listing of references relating to a given Fact was not attempted; the aim was to summarize the current state-of-knowledge of the field not to provide a comprehensive list of published references. In addition, this site contains a number of reviews, some of which overlap in content with BCGD. Gene expression profiling is a technique used in molecular biology to query … CGAP (Kuska, 1996) is an extremely important project whose goal is to characterize the changing expression of a large number of genes as normal cells develop into tumor cells. 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. 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. For example, the localization of BRCA1 to the nucleus was a well-known controversy for a year or so. 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. In addition, data extracted from papers rather than abstracts will frequently be absent from its PubMed citation. If you have a very strong family history of certain cancers, there might be a faulty gene in your family that increases your risk of breast cancer. The BReast CAncer genes database is built for world-wide use. Described in Results.) (In this and the next three figures, the browser's (Netscape's) navigation tools have been hidden). The current editorial board of BCGD is listed at http://mbcr.bcm.tmc.edu/ermb/bcgd/bcgd.html. Genes that increase the risk of breast cancer are BRCA1 and BRCA2. Operations Research, 43(4), pages 570-577, July-August 1995. BCGD can be searched either by gene name or keyword. View Dataset. INTRODUCTION Breast cancer is the most common non-skin type malignancy and the second leading cause of cancer mortality in women [1]. Breast cancer (BC), which is the most common malignant tumor in females, is associated with increasing morbidity and mortality. 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. In breast cancer, for example, more than 40 biomarkers have been proposed containing between 3 and 512 genes and whose prognostic or predictive performance depends on therapy, hormone receptor status, and the number of genes , . One of the serious impediments to achieving clinical benefits from this information however, is finding and assessing the significance of mutations … 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. Compared to books and reviews, digital resources can be more up-to-date, developed cumulatively, easier to use, and more powerful than their traditional predecessors. What is the KM plotter? Researchers have developed a variety of strategies to cope with an excessively large scientific literature. The recent identification of mutations in breast cancer susceptibility genes has provided the exciting opportunity to help identify women who are at high risk to develop breast cancer. Our syndication services page shows you how. 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. The result of a keyword search organizes Facts first by Gene Name, and then by Topic within a gene. These can be eliminated by using the Boolean AND term to combine the gene name search with a tumor gene specific search. Six breast cancer datasets, … Restricting this list to those citations relevant to breast cancer genes requires a two part strategy. Breast cancer cell line MDA-MB-453 response to DHT Species: human … 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. . For cancer to develop, genes regulating cell growth and differentiation must be altered; these mutations are then maintained through subsequent cell divisions and are thus present in all cancerous cells. BCGD is located at http://mbcr.bcm.tmc.edu/ermb/bcgd/bcgd.html. 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. An International Collaborative Effort hosted by NHGRI. 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. BCGD contains a comprehensive list of genes involved in breast cancer, and for each of these genes, information on a specific set of topics. The data, which has already lead to improvements in our ability to diagnose, treat, and prevent cancer, will remain publicly available for anyone in the research community to use. 27: 12–17. 1American Cancer Society. To reduce that effect, a `low stringency search' was developed which by itself is not very useful in that only 25% of the citations retrieved are relevant to tumor genes, but when combined with a gene name returns about 75% of the relevant papers. "You did a great service to the cancer research community and by that to the patients that donated the samples!." For some of these names, a large number of irrelevant citations are retrieved, e.g. Philadelphia, Pa: Lippincott Williams & Wilkins; 2005: 1420. To that end, BCGD is structured to accommodate future development. 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. It contains several infos base by base, amino acid by amino acid on the breast cancer genes coding sequence. As described in Materials and methods, making these searches reasonably complete required searching by gene, using all the names by which that gene is known. 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. (An analogous comparison is between a dictionary and a book containing the same words and definitions in random order). The Breast Cancer Gene Database: a collaborative information resource. A list of Topics used in BCGD is shown in Table 2. i cation of breast cancer types that is implied by the e ectiveness of the Oncotype DX and PAM50 gene sets. However, the prognostic significance of RRM2 gene in breast cancer remains to be investigated. 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. From these analysis we created two gene lists for each subtype of TNBC, genes containing genetic variants (GWAS genes) and genes without genetic variants (non-GWAS genes). 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. David A Wheeler. The 2270 facts in BCGD have been extracted from 134 different journals. Data entry screen for BCGD. Each subtype is associated with a unique panel of mutated genes. Data in BCGD is linked to other on-line resources such as Entrez, GeneCards and On-Line Mendelian Inheritance in Man. 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Collaborative information resource biological processes associated BRCA mutations browser 's ( Netscape 's ) navigation have. Ducts of the papers published on these genes data base and BRCA2 MA, Lopez R and Sterk P. reviews!
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