Post by Max on Oct 10, 2005 18:49:39 GMT -5
Introduction for the beginner: Gene Databases
When studying the (side)-effects of (Ro)accutane, there are many similarities between at a first glance very different effects. One of the causes to this is the gene-expression. One gene that is expressed in the skin can also be widely expressed in cells in the brain, liver, kidneys, heart and many more cells. This is the case with the retinoid X receptor, RXR - that is shown to be heavily affected by the retinoid 13-cis-retinoic acid (Roaccutane). This means that when the substance is used in a very high dose, all cells that carry these receptors are going to be affected. As an example, let us take a look at this retinoid receptor by looking in a Gene Database.
- Click link -
Genecards - RXRA
RXR exists in three forms. We are going to take a look at RXRalpha (RXRA).
Where is the gene expressed?
The genecard for RXRA contains a box where the expression of the receptor is listed in different parts of the body. (Says "tissue" "clones per gene" "total clones"). A high expression means that there are many copies of the receptor.
Related genes
This is a very useful section, because if a gene is related in structure (has a sequence that reminds about the gene that is searched for), in this case RXRA, we find that these genes also are very likely to be affected. In the case of RXRA, since we know it is affected, we can find out that other receptors within these families with high certainity also are affected. In this case it turns out that RXRA has many related genes, and also is found to affect many genes secondarily:
InterPro Domains and Families:
IPR008946 Str_ncl_receptor
IPR000003 RtnoidX_receptor
IPR001628 Znf_C4steroid
IPR001723 Stdhrmn_receptor
IPR000536 Hrmon_recept_lig
Sequences
Generally the sequences (of "small amino-acids" - nucleic acids, of which the gene consists) do not tell a whole lot, if not analysed with powerful computerized tools. However, some short sequences may reveal a bit about binding of residues and transcription.
Size
Different genes have different sizes.
Other information
The gene-card contains much more good information, such as references to studies done on the gene, similarities in different species and more. Genecards are powerful tools in biochemical research, and many databases are available to the public.
When studying the (side)-effects of (Ro)accutane, there are many similarities between at a first glance very different effects. One of the causes to this is the gene-expression. One gene that is expressed in the skin can also be widely expressed in cells in the brain, liver, kidneys, heart and many more cells. This is the case with the retinoid X receptor, RXR - that is shown to be heavily affected by the retinoid 13-cis-retinoic acid (Roaccutane). This means that when the substance is used in a very high dose, all cells that carry these receptors are going to be affected. As an example, let us take a look at this retinoid receptor by looking in a Gene Database.
- Click link -
Genecards - RXRA
RXR exists in three forms. We are going to take a look at RXRalpha (RXRA).
Where is the gene expressed?
The genecard for RXRA contains a box where the expression of the receptor is listed in different parts of the body. (Says "tissue" "clones per gene" "total clones"). A high expression means that there are many copies of the receptor.
Related genes
This is a very useful section, because if a gene is related in structure (has a sequence that reminds about the gene that is searched for), in this case RXRA, we find that these genes also are very likely to be affected. In the case of RXRA, since we know it is affected, we can find out that other receptors within these families with high certainity also are affected. In this case it turns out that RXRA has many related genes, and also is found to affect many genes secondarily:
InterPro Domains and Families:
IPR008946 Str_ncl_receptor
IPR000003 RtnoidX_receptor
IPR001628 Znf_C4steroid
IPR001723 Stdhrmn_receptor
IPR000536 Hrmon_recept_lig
Sequences
Generally the sequences (of "small amino-acids" - nucleic acids, of which the gene consists) do not tell a whole lot, if not analysed with powerful computerized tools. However, some short sequences may reveal a bit about binding of residues and transcription.
Size
Different genes have different sizes.
Other information
The gene-card contains much more good information, such as references to studies done on the gene, similarities in different species and more. Genecards are powerful tools in biochemical research, and many databases are available to the public.