WormBase Model:Gene regulation

WormBase Models

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

Unused tags

Evidence

Cis_regulator_seq

Cis_regulated_seq