WormBase Model:Gene regulation
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Model
////////////////////////////////////////////////////////////////////////////////////////////// // // ?Gene_regulation class - Wen 05082003// ////////////////////////////////////////////////////////////////////////////////////////////// // 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 //Added by wen 02132006 to distinguish regulation of expression level or localization. Change_of_expression_level //Added by wen 02132006 Molecule_regulator ?Molecule XREF Gene_regulator #Boolean // ?Molecule model - Karen Yook Regulation_level Transcriptional //Added by wen 02132006 to distinguish process that regulation occurs on Post_transcriptional //Added by wen 02132006 Post_translational //Added by wen 02132006 Regulator Regulator_info Allele ?Variation RNAi ?RNAi XREF Gene_regulation Trans_regulator_gene ?Gene XREF Trans_regulator #Boolean Trans_regulator_seq ?CDS XREF Trans_regulator #Boolean Cis_regulator_seq ?Sequence XREF Cis_regulator #Boolean Other_regulator ?Text #Boolean Target Target_info Expr_pattern ?Expr_pattern Trans_regulated_gene ?Gene XREF Trans_target #Boolean Trans_regulated_seq ?CDS XREF Trans_target #Boolean Cis_regulated_seq ?CDS XREF Cis_target #Boolean Other_regulated ?Text #Boolean Associated_feature ?Feature XREF Associated_with_gene_regulation #Evidence //to curate sequence feature connection [ar2] Result Positive_regulate #GR_condition Negative_regulate #GR_condition Does_not_regulate #GR_condition // addded to capture negative data [040220 krb] Remark ?Text #Evidence Reference ?Paper XREF Gene_regulation
Proposed Changes
Unused tags
Evidence
Cis_regulator_seq
Cis_regulated_seq