Difference between revisions of "Sequence Feature"
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== Rules for marking up regions== | == Rules for marking up regions== | ||
| − | *If a region is necessary and sufficient to drive a reporter gene, then | + | *If a region is necessary and sufficient to drive a reporter gene, then mark it as an 'enhancer' or 'silencer'. |
| − | mark it as an 'enhancer' or 'silencer'. | ||
| − | *If a region is both an enhancer and a silencer, then it should have | + | *If a region is both an enhancer and a silencer, then it should have the SO_term tags for both of these. |
| − | the SO_term tags for both of these. | ||
| − | *If mobility shift experiments or similar experimental evidence is | + | *If mobility shift experiments or similar experimental evidence is available to assert that a short region is a TF binding site, then mark it as a TF_binding_site. |
| − | available to assert that a short region is a TF binding site, then | ||
| − | mark it as a TF_binding_site. | ||
| − | *Similarity to a known binding motif is not evidence of being a | + | *Similarity to a known binding motif is not evidence of being a TF_binding_site. |
| − | TF_binding_site. | ||
| − | *If there is no evidence for a TF binding site and it has an effect on | + | *If there is no evidence for a TF binding site and it has an effect on expression when mutated or deleted, but is not sufficient to drive a reporter gene, then we cannot assert that it is an enhancer or a TF binding site. Mark it as an anonymous 'regulatory_region'. |
| − | expression when mutated or deleted, but is not sufficient to drive a | ||
| − | reporter gene, then we cannot assert that it is an enhancer or a TF | ||
| − | binding site. Mark it as an anonymous 'regulatory_region'. | ||
| − | *If a region has the properties of being both a TF binding site and an | + | *If a region has the properties of being both a TF binding site and an enhancer then mark it up as two Features, one a TF_binding_site and one an enhancer. |
| − | enhancer then mark it up as two Features, one a TF_binding_site and | ||
| − | one an enhancer. | ||
| − | *If a region is asserted to be a promoter region in the paper and it is | + | *If a region is asserted to be a promoter region in the paper and it is within 200bp (or thereabouts?) of the 5' of the target gene and it is neccessary and sufficient to promote a reporter gene, mark it as a promoter. If in doubt, consider marking it as an enhancer. |
| − | within 200bp (or thereabouts?) of the 5' of the target gene and it is neccessary and | ||
| − | sufficient to promote a reporter gene, mark it as a promoter. If in | ||
| − | doubt, consider marking it as an enhancer. | ||
Revision as of 08:40, 30 July 2013
Rules for marking up regions
- If a region is necessary and sufficient to drive a reporter gene, then mark it as an 'enhancer' or 'silencer'.
- If a region is both an enhancer and a silencer, then it should have the SO_term tags for both of these.
- If mobility shift experiments or similar experimental evidence is available to assert that a short region is a TF binding site, then mark it as a TF_binding_site.
- Similarity to a known binding motif is not evidence of being a TF_binding_site.
- If there is no evidence for a TF binding site and it has an effect on expression when mutated or deleted, but is not sufficient to drive a reporter gene, then we cannot assert that it is an enhancer or a TF binding site. Mark it as an anonymous 'regulatory_region'.
- If a region has the properties of being both a TF binding site and an enhancer then mark it up as two Features, one a TF_binding_site and one an enhancer.
- If a region is asserted to be a promoter region in the paper and it is within 200bp (or thereabouts?) of the 5' of the target gene and it is neccessary and sufficient to promote a reporter gene, mark it as a promoter. If in doubt, consider marking it as an enhancer.
