WormBase Model:Gene regulation
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Model
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//
// ?Gene_regulation class - Wen 05082003//
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// Gene regulation model describes the expression pattern in different genetic backgrounds
// "Summary" use text to describe the experimental results observed from experiments. It should be summarized from
// publication or pers. coomunication.
// "Method" is the experimental approach, whether it is done by Immunostaining, Reporter_gene or ...
// "Regulator" is the party that regulated the expression pattern, it can be a gene (Trans_regulator), a short
// DNA sequence (Cis_regulator), or protein, drug, condition ... (Other_regulator).
// Regulator_info describes details about regulator, such aswhat allele and what RNAi is used to test the regulation.
// "Target" is the party that displayed expression pattern, can be a gene(Trans_regulated) or a specific promoter
// sequence(Cis_regulated). Target_info described what Expr_pattern is tested under mutant background. Here the
// Expr_pattern refers to the expression pattern under wild type C. elegans background.
// Result: "Positive_regulate" display when and where increase of expression were observed. "Negative_regulate" display
// when and where decrease of expression were observed.
// "Remark" is for any other information that might be useful.
// "Evidence" will be used to curate data from personal communication.
//"Reference" show which paper is the source of the data.
?Gene_regulation Evidence #Evidence //Not used
Summary ?Text //"Summary" use text to describe the experimental results observed from experiments. It should be summarized from publication or pers. coomunication.
Method Antibody ?Text// "Method" is the experimental approach, whether it is done by Immunostaining, Reporter_gene or ...
Antibody_info ?Antibody XREF Gene_regulation
Reporter_gene ?Text
Transgene ?Transgene XREF Gene_regulation
In_situ Text
Northern Text
Western Text
RT_PCR Text
Other_method ?Text
Type Change_of_localization //distinguish regulation of expression level or localization.
Change_of_expression_level
Molecule_regulator ?Molecule XREF Gene_regulator #Boolean // ?Molecule model - Karen Yook
Regulation_level Transcriptional //distinguish process that regulation occurs on
Post_transcriptional
Post_translational
Regulator Regulator_info Allele ?Variation //Allele that regulates the expression
RNAi ?RNAi XREF Gene_regulation //RNAi that regulates the expression
Trans_regulator_gene ?Gene XREF Trans_regulator #Boolean //Gene that regulates the expression
Trans_regulator_seq ?CDS XREF Trans_regulator #Boolean //this is not used any more
Cis_regulator_seq ?Sequence XREF Cis_regulator #Boolean //this is not used any more
Other_regulator ?Text #Boolean //for other regulation such as heat shock
Target Target_info Expr_pattern ?Expr_pattern //expression pattern in wild type background
Trans_regulated_gene ?Gene XREF Trans_target #Boolean //regulated gene
Trans_regulated_seq ?CDS XREF Trans_target #Boolean //not used any more
Cis_regulated_seq ?CDS XREF Cis_target #Boolean/ /not used any more
Other_regulated ?Text #Boolean //not used any more
Associated_feature ?Feature XREF Associated_with_gene_regulation #Evidence //to curate sequence feature connection [ar2]
Result Positive_regulate #GR_condition //these tags indicate regulation type
Negative_regulate #GR_condition
Does_not_regulate #GR_condition // addded to capture negative data [040220 krb]
Remark ?Text #Evidence //all other related info
Reference ?Paper XREF Gene_regulation //primary article that the data were published
Proposed Changes
Unused tags
Evidence
Cis_regulator_seq
Cis_regulated_seq
