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 mark it as an 'enhancer' or 'silencer'. | *If a region is necessary and sufficient to drive a reporter gene, then mark it as an 'enhancer' or 'silencer'. | ||
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*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. | *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. | ||
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+ | == Link to Expression pattern == | ||
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+ | == Link to Gene Regulation == |
Revision as of 08:42, 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.