Cancer Letters 77 (1994) 163-171. 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. In: DeVita VT Jr, Hellman S, Rosenberg SA ed. Equally, an example of an important disease entity which does not significantly … The function of the BRCA genes is to repair cell damage and keep breast, ovarian, and other cells growing normally. Described in Results.) 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. 27: 18–24. This generates a list of genes mostly consisting of and containing most of the breast cancer genes that are transcription factors. For example, the localization of BRCA1 to the nucleus was a well-known controversy for a year or so. This cancer starts in the tissues of the breast. 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. Using the Web-based data entry form (Figure 2), curators can enter information into the database, either from the Abstract or from a (separate) full text copy of the paper. 1999 Nucleic Acids Res. Thus, this initial search is used primarily to develop and maintain the list of Breast Cancer genes. 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). Genes containing genetic variants associated with an increased risk of developing breast cancer were identified using gene names and corresponding gene symbols. 1999 Nucleic Acids Res. (In this and the next three figures, the browser's (Netscape's) navigation tools have been hidden). 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. Basal-like subtype shares many genetic features with high-grade serous ovarian cancer, suggesting that the cancers have a common … 27: 95–98. 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. TCGA's original breast cancer study and expanded study with focus on ductal versus lobular subtypes, Find NCI-supported breast cancer clinical trials. Benson DA, Boguski MS, Lipman DJ, Ostell J, Ouellette BF, Rapp BA and Wheeler DL. 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. More recently, digital resources have provided additional solutions to this problem. A link provides access to Facts previously entered by any of the curators so that duplicate entries can be avoided. 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. This cancer develops in the breast milk-producing lobules or glands. Access to the data entry forms is password protected and thus is available only to curators. The BReast CAncer genes database is built for world-wide use. It gives information on tumor features such as tumor size, density, and texture. 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. 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. Number of PubMed citations about breast cancer genes. Men can also have breast cancer, although male breast cancer is rare. 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. Buhle Jr EL, Goldwein JW and Benjamin I. . 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. Restricting this list to those citations relevant to breast cancer genes requires a two part strategy. Result of a keyword search using receptor as the query term. Currently, BCGD supports hypertext links to OMIM and PubMed. Our syndication services page shows you how. ... BRCA1-related gene signature in breast cancer: the role of ER status and molecular type Species: human Samples: 41 Factors: 7 Tags: basal, brca1, breast, breast cancer, cancer, disease, estrogen, liquid, luminal, ovarian cancer, protein, sporadic breast cancer. BCGD is freely available via the Web. What have TCGA researchers learned about breast cancer? For this application, the editorial functions built in to the system could be used to ensure adequate peer review of information published this way. 1998 Bioinformatics 14: 656–664. Cancer Inst. 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. 25: 14–17. 2Wood WC, Muss HB, Solin LJ, Olopade OL: Malignant Tumors of the Breast. Effective treatments include surgery, chemotherapy, radiotherapy, endocrinotherapy and molecular-targeted therapy. 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. . Conflicting data are often apparent in the fact lists. because the gene name rasH matches the medically common word rash. 1994 Proceedings–Eighteenth Annual Symposium on Computer Applications in Medical Care. It is more of a research project than an information resource. Researchers have developed a variety of strategies to cope with an excessively large scientific literature. 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. 1999 Nucleic Acids Res. 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. BCGD can be searched either by gene name or keyword. All words in the Fact and Comment fields of the database can be searched by Keyword. We developed a gene signature based on G9a-suppressed genes as a measure of G9a activity for patient stratification and G9a-based therapy by using the integration of in silico data available through breast cancer gene expression databases, combined with the use of small molecule inhibitors as a potential therapeutic agent. The Genes-to-Systems Breast Cancer Database lists breast cancer genes correlated with the cell cycle process. Want to use this content on your website or other digital platform? Because the facts in BCGD are extracted from the published literature, it is important to begin by identifying breast cancer gene publications. https://doi.org/10.1038/sj.onc.1203335, DOI: https://doi.org/10.1038/sj.onc.1203335, Journal of Bioinformatics and Computational Biology The fact may be taken from a primary research paper, from the PubMed abstract of a primary research paper, or from a review. This initial search misses many references which concern a Breast Cancer Gene, but which report results which themselves are not particular to Breast Cancer. Facts pertaining to Cell Location and Cell Type Distribution are visible in this figure. The Fact entry form contains fields for selecting the Fact type (Table 2) and entering the brief statement of fact and longer comments where required. 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. Information in the database consists of collections of Facts organized by Topic. It is possible to search OMIM with the words `Breast Cancer' and retrieve a list of 148 records, where most records correspond to a gene. 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. OMIM is the resource that probably has greater overlap with BCGD than any other. 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. BCGD is located at http://mbcr.bcm.tmc.edu/ermb/bcgd/bcgd.html. 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. 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. 27: 12–17. The recent advent of cyclin-dependent kinase (CDK) 4/6 inhibitors palbociclib and ribociclib has represented a major step forward for patients with hormone receptor-positive breast cancer. 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 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. About 10% of all cases of advanced breast cancer2 are invasive lobular breast carcinoma. 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). The genes we talk about when it comes to genetic testing for breast cancer— commonly known as BRCA-1 and BRCA-2 — are normal genes we all have, which act as tumor suppressors. The Web-based data entry interface allows data to be entered into BCGD from anywhere in the world. Given the wide variety of traditional and digital resources available to the breast cancer researcher, what additional benefits can be derived from BCGD? View Dataset. For some of these names, a large number of irrelevant citations are retrieved, e.g. Thus, in a practical sense, these also overlap little with BCGD. 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. Sequencing data from Breast Cancer samples : Illumina Genome Analyzer II : 1 : EGAD00000000054: NCI-H209 is an immortal cell line derived from a bone marrow metastasis of a patient with small cell lung cancer, taken before chemotherapy. Methods: RRM2 expression was initially evaluated using the Oncomine database. Ohkawa H, Ostell J and Bryant S. . 103–107. Additional information on breast cancer. Correspondence to an older fact). Gene expression profiling-based molecular classification of breast cancers predicts the general clinical behavior of breast cancers corresponding to the different molecular subtypes. Kuska B. . 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. In addition, data extracted from papers rather than abstracts will frequently be absent from its PubMed citation. To that end, BCGD is structured to accommodate future development. A list of Topics used in BCGD is shown in Table 2. Operations Research, 43(4), pages 570-577, July-August 1995. Breast cancer cell line MDA-MB-453 response to DHT Species: human … 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. As others have pointed out, there is no single "mutated gene sequence responsible for breast cancer". Thus, the development of the database is envisioned to be a cooperative work of scientists, editors, curators and authors, regardless of their location. Blake JA, Richardson JE, Davisson MT and Eppig JT. 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 entry screen for BCGD. 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. Atlanta: American Cancer Society, Inc. 2010. In addition, this site contains a number of reviews, some of which overlap in content with BCGD. 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. Machine learning techniques to diagnose breast cancer from fine-needle aspirates. Cancer Facts and Figures 2010. 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 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. 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. 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. 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. With the development of molecular biology, immunology and pharmacogenomics, an increasing amount … To obtain (2017), Oncogene Thank you for visiting nature.com. 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]). Every fact in the database is linked to a journal citation. i cation of breast cancer types that is implied by the e ectiveness of the Oncotype DX and PAM50 gene sets. 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. 1). The Gene name is listed at the top of the page along with relevant synonyms. Philadelphia, Pa: Lippincott Williams & Wilkins; 2005: 1420. BCGD offers both short and long term benefits to the breast cancer gene research community. 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. McGraw Hill, Inc pp. 1997 Nucleic Acids Res. Each subtype is associated with a unique panel of mutated genes. 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. David A Wheeler. 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. Mangasarian. The result of this search will be a list of genes which is a good approximation of all transcription factors (Figure 4). NCI-BL209 is an EBV … Each subtype is associated with a unique panel of mutated genes. Data used: Kaggle-Breast Cancer Prediction … There is very little overlap between BCGD and CGAP; both are important to breast cancer researchers. A wide variety of such resources are available to the breast cancer gene research community, ranging from repositories of primary data (e.g. 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. Some of this information concerns identification of and sources for important reagents (e.g. 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. Baasiri, R., Glasser, S., Steffen, D. et al. Rebhan M, Chalifa-Caspi V, Prilusky J and Lancet D. . BCGD currently contains approximately 2270 facts from 1162 publications describing 60 genes identified as breast cancer genes. After a fact has been entered into the database, it is flagged as `pending' and withheld from public view until one or more database editors have reviewed it. 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. TCGA focused mainly on two types of invasive breast cancer: ductal carcinoma and lobular carcinoma. The individual Facts originate from a variety of sources. Aside from risk of disease, there are SNPs that play a role in how patients respond to drugs used to treat breast cancer. 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 . Unless augmented with further evidence for oncogenicity, genes that only manifest aberrant regulation in breast neoplasms are not included in the database. 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. Genes that increase the risk of breast cancer are BRCA1 and BRCA2. The following sections present … 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. This site is best viewed with Chrome, Edge, or Firefox. A somewhat complicated search strategy, described in Materials and methods, was found to be necessary for the comprehensive retrieval of these citations. 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. "You did a great service to the cancer research community and by that to the patients that donated the samples!." 88: 1801–1803. Breast cancer (BC), which is the most common malignant tumor in females, is associated with increasing morbidity and mortality. 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. . We detected you are using Internet Explorer. Invasive ductal carcinoma is the most common type of breast cancer. There are plans to create a prostate and colon-specific extensions of TGDB as well. It contains several infos base by base, amino acid by amino acid on the breast cancer genes coding sequence. Facts are often redundant; a particular fact, such as molecular weight or subcellular localization, may have been reported independently by different laboratories and as a result the fact is duplicated in BCGD with the duplicates having different citations. INTRODUCTION Breast cancer is the most common non-skin type malignancy and the second leading cause of cancer mortality in women [1]. Currently, searches with multiple keywords are treated as a logical `OR'. The current editorial board of BCGD is listed at http://mbcr.bcm.tmc.edu/ermb/bcgd/bcgd.html. On a higher level, breast cancer datasets collected by different institutions can be considered as resamplings from the underlying breast cancer population. However, the prognostic significance of RRM2 gene in breast cancer remains to be investigated. 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. Facts are brief statements of findings, limited to 80 characters. Individual facts are listed below, organized by Topic. 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. PubMed Google Scholar. We know about several gene faults that can increase breast cancer risk and there are tests for some of them. Datasets are collections of data. (An analogous comparison is between a dictionary and a book containing the same words and definitions in random order). 7th ed. 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. Digital platform FDA labels, NCCN and other tumor gene databases are actively being recruited ; contact information derived! Type malignancy and the second cause of cancer mortality in women [ 1 ] most frequently diagnosed cancer the. Addition contain a small amount of direct information about the gene name or keyword best viewed with,... Described in Materials and methods, was found to be entered into BCGD from anywhere in the meantime to! A well-known controversy for a gene a listing of all genes in BCGD are extracted from the Machine. Rather they are left in for the reproducibility of the given fact ( analogous... 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'S ( Netscape 's ) navigation tools have been hidden ) UCI Machine learning Repository only manifest aberrant in... To be entered into BCGD from anywhere in the meantime, to ensure continued,... Snps that play a role in how patients respond to drugs used to some... It comprises about 65–85 % of breast cancer gene database transcription factors ( figure 4 ), an example of an tool...