Genes beta

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Genes beta 2017-11-07T23:54:41+00:00

Genes Beta

Welcome to the first version of Genes beta, a subdatabase carved from the Modern Medical Dictionary Database (MMDD), a curated resource for students, practitioners and scientists in biology, medicine and the health professions. This is the second product to be spun off The Modern Medical Dictionary (MMD) database, which is linked to the website www.newmedicalterms.com.

When the human genome was first sequenced in 2003, no one knew how many genes they’d find. At the time, the best guess-timates put the number at 100,000. As the genomic information was fine tuned, the number has steadily dropped to the current number of 23,000-ish genes. This App includes useful information on a bit over 8,000 of those genes which I’ve come across in my reading of the literature.

In deciding what constitutes “useful information” on a gene, I felt that three blocks of information would be of particularly useful to advanced biomedical consumers. The amount of information on each gene intentionally skates between an anemic offerings in a standard medical dictionary—assuming one could actually find anything about a particular gene—and an exhaustive treatise on a particular gene or gene product found in the Genecards, UniProt and OMIM databases.

I’ll use the BRAF gene as an example of the information you’ll find in most of the Genes in this “App”

BRAF 

Block 1—Definition 

The gene on chromosome 7q34 that encodes B-Raf proto-oncogene—serine/threonine kinase (OMIM:164757, UniProtKB:P15056), a protein of the raf/mil family of serine/threonine protein kinases, which play a key role in regulating the MAP kinase/ERKs signalling pathway, affecting cell division, differentiation, and secretion.

Molecular pathology Defects of BRAF cause

• Cardiofaciocutaneous syndrome 1 (OMIM:115150)

• LEOPARD syndrome 3 (OMIM:613707)

• Noonan syndrome 7 (OMIM:613706)

Acquired BRAF mutations have been linked to non-Hodgkin lymphoma, colorectal cancer, melanoma, thyroid carcinoma, non-small cell lung carcinoma, and adenocarcinoma of lung.

Explanation The (above) definition block indicates:

  • The chromosome on which the gene is found (here, 7q34)

  • The protein product’s currently preferred name (these often change over time, here, B-Raf proto-oncogene—serine/threonine kinase, which is listed in bold, simply because some of the names are fairly long)

  • The OMIM* and UniProt† numbers assigned to the protein product (here, OMIM:164757,

    UniProtKB:P15056)

  • Details of interest about the gene product (here, a protein of the

    raf

    /mil family of serine/threonine protein kinases, which play a key role in regulating the MAP kinase/ERKs

    signalling

    pathway, affecting cell division, differentiation, and secretion). The details are a composite of the information from the Summaries section of the relevant Genecards entry. I’ve found that those sections are not always written in the best English

*Online Mendelian Inheritance in Man catalog, which is produced by workers at Johns Hopkins

†UniProt database of protein sequence and functional information. The  UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR

For those genes that have been linked to one or more specific disorders, I added a second paragraph labelled Molecular pathology, which lists the disease or diseases caused by defects in the defined gene and the relevant OMIM catalogue number, here,

• Cardiofaciocutaneous syndrome 1 (OMIM:115150)

• LEOPARD syndrome 3 (OMIM:613707)

• Noonan syndrome 7 (OMIM:613706)

The reader will note that the disorder is followed by the relevant OMIM catalog number. In some cases, the gene may be associated in a more generic fashion to an array of conditions including cancer, diabetes, rheumatoid arthritis and the association is not completely mendelian, but rather presence of a defect in the gene alters susceptibility to that condition, here, Acquired BRAF mutations have been linked to non-Hodgkin lymphoma, colorectal cancer, melanoma, thyroid carcinoma, non-small cell lung cancer, and adenocarcinoma of the lung.

Block 2—Synonyms

B-Raf proto-oncogene—serine/threonine kinase,

V-Raf Murine Sarcoma Viral Oncogene Homolog B1,

V-Raf Murine Sarcoma Viral Oncogene Homolog B,

Proto-Oncogene B-Raf,

BRAF1,

RAFB1,

B-Raf Proto-Oncogene Serine/Threonine-Protein Kinase (P94),

Murine Sarcoma Viral (V-Raf) Oncogene Homolog B1,

94 KDa B-Raf Protein,

EC 2.7.11.1,

B-RAF1,

P94,

NS7,

The second block of information is simply a list of names (aliases, synonyms) by which the gene has been known in the past, with the currently preferred name for the gene’s protein product written in bold, and is taken verbatim from the aliases section of the corresponding Genecards entry. Current medical dictionaries* have traditionally addressed aliases and synonyms by creating separate entries for the aliases and synonyms, which falsely elevates the number of entries in these works.

*Dorland’s Illustrated Medical Dictionary, Mosby’s Dictionary of Medicine, Nursing & Health Professions, LStedman’s Medical Dictionary, Taber’s Cyclopedic Medical Dictionary

As an example of how other medical dictionaries address aliases, on page 533 of the current edition of the Dorland’s, there are 41 aliases listed–e.g., Folling disease (better known as phenylketonuria), Francis disease (tularemia), Frommel disease (Chiari-Frommel disease), and Gee-Thaysen disease (adult coeliac disease); 15 diseases on page 533 are actually defined. Over time, in addition to deleting the reference numbers from each alias (already done), this work will eliminate the inappropriate global capitalization of each word) and alphabetize the list, with the primary name remaining in bold, so eventually the above list will appear as written below.

94 KDa B-Raf protein

B-Raf proto-oncogene—serine/threonine kinase

B-Raf proto-oncogene serine/threonine-protein kinase (P94)

B-RAF1

BRAF1

EC 2.7.11.1

murine sarcoma viral (v-Raf) oncogene homolog B1

NS7

P94

proto-oncogene B-Raf

RAFB1

v-Raf murine sarcoma viral oncogene homolog B1

v-Raf murine sarcoma viral oncogene homolog B

Block 3—References

www.genecards.org/cgi-bin/carddisp.pl?gene=BRAF

http://www.uniprot.org/uniprot/P15056

Any project of this scale, especially when written entirely by one author, cannot escape the need for references, which have been included since its inception in 1984, nearly 33 years ago when I began. With few exceptions, every gene included in this beta has at least two references, one to the Genecards database* compiled and maintained at the Weizmann Institute in Rehovot, Israel, and other to the UniProt database† compiled in Geneva, Hinxton, UK and Washington DC. The references are included so the reader can efficiently jump to a peer-reviewed and curated source of further information.

*Which contains genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes †Which contains protein sequence and functional information

How to use this resource. 

You should find it easy to email yourself the information on any of the genes, for which we ask that you register. Your registration will enable us to give you a heads up when we release other products. We will not share your information with (annoying) third parties. If you want a particular gene or genes which is not currently in the beta, shoot me an email to (jcsegenmd@yahoo.com) and I’ll make sure it goes in the update.

Future plans for the Genes beta. 

The Genes subdatabase currently has useful information on one-third of the known human genes, a point which we feel makes it a useful resource. We expect to release updates to the Genes beta on a regular basis, let’s say, every time another 1500 genes are added; the timeframe for these updates is up in the air, but should occur at least every 6 months. If you feel we’ve missed important genes, send an email directly to me jcsegenmd@yahoo.com and I’ll make sure it goes in the update.

Best regards

JC Segen, MD, FCAP

Kent Hummel, Principal, Plus 1 Marketing Solutions