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. 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. The 2270 facts in BCGD have been extracted from 134 different journals. (The database used by PubMed is a superset of the MEDLINE database; http://www.ncbi.nlm.nih.gov/PubMed/overview.html.). These consist largely of links to various information resources, and in addition contain a small amount of direct information about the gene. 27: 49–54. View Dataset. --Clinical pathologist, Karolinska University Hospital 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. In addition, data extracted from papers rather than abstracts will frequently be absent from its PubMed citation. The current editorial board of BCGD is listed at http://mbcr.bcm.tmc.edu/ermb/bcgd/bcgd.html. 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. For example, the localization of BRCA1 to the nucleus was a well-known controversy for a year or so. Moreover, GOBO offers the possibility of investigation of gene expression levels in breast cancer subgroups and breast cancer cell lines for gene … Gene set enrichment analysis (GSEA) was used to analyze some enriched pathways and biological processes associated BRCA mutations. Published, Pending, On Hold. For this application, the editorial functions built in to the system could be used to ensure adequate peer review of information published this way. David A Wheeler. Philadelphia, Pa: Lippincott Williams & Wilkins; 2005: 1420. Data in BCGD is linked to other on-line resources such as Entrez, GeneCards and On-Line Mendelian Inheritance in Man. The Breast Cancer Gene Database: a collaborative information resource. To obtain For some of these names, a large number of irrelevant citations are retrieved, e.g. 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 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. This cancer starts in the tissues of the breast. The PubMed database (http://www.ncbi.nlm.nih.gov/Entrez/medline.html) was searched for citations to these publications. 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. 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. Facts pertaining to Cell Location and Cell Type Distribution are visible in this figure. What is the KM plotter? Additional information on breast cancer. These can be eliminated by using the Boolean AND term to combine the gene name search with a tumor gene specific search. 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). 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. 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. 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 somewhat complicated search strategy, described in Materials and methods, was found to be necessary for the comprehensive retrieval of these citations. Our syndication services page shows you how. transgenic mice) which overlaps little with BCGD. An important tool towards reaching that goal is a strategy for identifying all of the papers published on these genes. 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. The first part of that strategy combines the above search with: ``Breast Neoplasms'' [MESH TERMS] using the AND Boolean operator. A wide variety of such resources are available to the breast cancer gene research community, ranging from repositories of primary data (e.g. 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). Equally, an example of an important disease entity which does not significantly … 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. The data … Restricting this list to those citations relevant to breast cancer genes requires a two part strategy. BCGD curators used a combination of traditional browsing techniques and the PubMed search described above to identify publications from which to extract facts. This generates a list of genes mostly consisting of and containing most of the breast cancer genes that are transcription factors. 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. 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). 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/). (2018), BMC Bioinformatics You are using a browser version with limited support for CSS. 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 individual Facts originate from a variety of sources. 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 1995 Ismb 3: 259–267. ... 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. 1999 Nucleic Acids Res. Basal-like subtype shares many genetic features with high-grade serous ovarian cancer, suggesting that the cancers have a common … 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. 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. The result of this search will be a list of genes which is a good approximation of all transcription factors (Figure 4). 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]). It is more of a research project than an information resource. 1999 Nucleic Acids Res. McGraw Hill, Inc pp. . Thus, this initial search is used primarily to develop and maintain the list of Breast Cancer genes. https://doi.org/10.1038/sj.onc.1203335, DOI: https://doi.org/10.1038/sj.onc.1203335, Journal of Bioinformatics and Computational Biology The cancer can be categorized into four molecular subtypes: HER2-enriched, Luminal A, Luminal B, and Basal-like. 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. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Breast cancer cell line MDA-MB-453 response to DHT Species: human … Indeed, worldwide, breast cancer accounts for almost 23% of all cancers (ex- The fact may be taken from a primary research paper, from the PubMed abstract of a primary research paper, or from a review. 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. (2020), Breast Cancer Research and Treatment 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. One of the serious impediments to achieving clinical benefits from this information however, is finding and assessing the significance of mutations … The specimen showed histologically typical small cells with classic neuroendocrine features. 25: 14–17. Given the wide variety of traditional and digital resources available to the breast cancer researcher, what additional benefits can be derived from BCGD? PubMed Google Scholar. The cancer can be categorized into four molecular subtypes: HER2-enriched, Luminal A, Luminal B, and Basal-like. 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. It comprises about 65–85% of all breast cancer and develops in the milk ducts of the breast. What have TCGA researchers learned about breast cancer? Facts are brief statements of findings, limited to 80 characters. Traditionally, this has included books and review articles which summarize a large volume of primary literature. We detected you are using Internet Explorer. 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. Unless augmented with further evidence for oncogenicity, genes that only manifest aberrant regulation in breast neoplasms are not included in the database. TCGA focused mainly on two types of invasive breast cancer: ductal carcinoma and lobular carcinoma. 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. 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. 1994 Proceedings–Eighteenth Annual Symposium on Computer Applications in Medical Care. Kuska B. . When this strategy was applied, citations to 90 373 publications were identified. An ENIGMA member is currently defined as a researcher or … 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. Genes containing genetic variants associated with an increased risk of developing breast cancer were identified using gene names and corresponding gene symbols. Bioreductive drugs, which are inactive drugs that become toxic to cancer cells under low oxygen conditions. About 10% of all cases of advanced breast cancer2 are invasive lobular breast carcinoma. This initial search misses many references which concern a Breast Cancer Gene, but which report results which themselves are not particular to Breast Cancer. The function of the BRCA genes is to repair cell damage and keep breast, ovarian, and other cells growing normally. 27: 12–17. "You did a great service to the cancer research community and by that to the patients that donated the samples!." 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. On the other hand, assessing the performance of proposed biomarkers in different populations or evaluating competing … 88: 1801–1803. On a higher level, breast cancer datasets collected by different institutions can be considered as resamplings from the underlying breast cancer population. Medical literature: W.H. 7th ed. Thus, in a practical sense, these also overlap little with BCGD. Primary facts are, of course, rare or absent from most reviews. 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. Gene expression profiling-based molecular classification of breast cancers predicts the general clinical behavior of breast cancers corresponding to the different molecular subtypes. BCGD can be searched either by gene name or keyword. H-ras, Hras, Ha-ras, rasH, etc.). 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. Because the facts in BCGD are extracted from the published literature, it is important to begin by identifying breast cancer gene publications. If you would like to reproduce some or all of this content, see Reuse of NCI Information for guidance about copyright and permissions. Cancer Letters 77 (1994) 163-171. 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. We know about several gene faults that can increase breast cancer risk and there are tests for some of them. 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. The genes most frequently identified in the separate resamplings were put forward as a ‘gold standard’. Invasive ductal carcinoma is the most common type of breast cancer. 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. For example, one could search with the keyword `transcription' and limit the search to the `Biochemical type'. 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. 1999 Nucleic Acids Res. In other words, a keyword search with `receptor kinase' will find all entries with either `receptor' or `kinase' in the fact or comment fields. Baasiri, R., Glasser, S., Steffen, D. et al. 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. 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. 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. BCGD contains a comprehensive list of genes involved in breast cancer, and for each of these genes, information on a specific set of topics. Described here is the Breast Cancer Gene Database (BCGD), an additional resource with unique benefits for breast cancer researchers. Atlanta: American Cancer Society, Inc. 2010. 27: 18–24. It offers the possibility to explore gene-expression of genes of interest in breast cancer. Effective treatments include surgery, chemotherapy, radiotherapy, endocrinotherapy and molecular-targeted therapy. 103–107. 27: 95–98. Result of a keyword search using receptor as the query term. 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. Data show that the engineered B cells expressing Bcl-x(L) exhibited progressively lower increases in apoptosis activation. It gives information on tumor features such as tumor size, density, and texture. 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. 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. Buhle Jr EL, Goldwein JW and Benjamin I. . 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