Difference between revisions of "WormBase Model:Gene regulation"
From WormBaseWiki
Jump to navigationJump to search (Created page with '__TOC__ WormBase Models == Curator Comments/Description == == Model == <pre> </pre> == Proposed Changes ==') |
(→Model) |
||
(2 intermediate revisions by 2 users not shown) | |||
Line 11: | Line 11: | ||
== Model == | == Model == | ||
<pre> | <pre> | ||
+ | ////////////////////////////////////////////////////////////////////////////////////////////// | ||
+ | // | ||
+ | // ?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 //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 | ||
</pre> | </pre> | ||
== Proposed Changes == | == Proposed Changes == | ||
+ | |||
+ | ==Unused tags== | ||
+ | |||
+ | Evidence | ||
+ | |||
+ | Cis_regulator_seq | ||
+ | |||
+ | Cis_regulated_seq |
Latest revision as of 21:15, 7 December 2010
Curator Comments/Description
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 //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