Gene Interaction

From WormBaseWiki
Jump to navigationJump to search

==Gene_gene Interaction OA==

OA interface

Interaction OA tab1.jpg

  • Tab 1
    • PGID
    • Interaction ID//generate automatically per entry
    • Non_directional //toggle on (default), off (color change by click) means effected/effector on.
    • Interaction Type//dropdown list with 11 types showing in .ace template
    • Effected Gene/Variation/Transgene//multiontology, corresponding to interactor in .ace file. order is not matter when dump to interactors
    • Effector Gene/Variation/Transgene//multiontology, corresponding to interactor in .ace file. order is not matter when dump to interactors


Interaction OA tab2.jpg

  • Tab 2
    • Curator//dropdown list
    • Paper//ontology
    • RNAi ID//free text fiel
    • Phenotype//multiontology
    • Remark//big text
    • Sentence ID//sentence shows in term info
    • False Positive//toggle, will not give an id or no dump if the sentence is false positive, containing no interaction info
    • next sentence button

.ace template:

  • Interaction : ""


  • Interactor "WBGene" Variation ""
  • Interactor "WBGene" Transgene ""
  • Interactor "WBGene"


  • Interaction_type Genetic Effector ""
  • Interaction_type Genetic Effected ""
  • Interaction_type Genetic Non_directional ""
  • Interaction_type Genetic Interaction_RNAi ""
  • Interaction_type Genetic Interaction_phenotype ""


  • Interaction_type Regulatory Effector ""
  • Interaction_type Regulatory Effected ""
  • Interaction_type Regulatory Non_directional ""
  • Interaction_type Regulatory Interaction_RNAi ""
  • Interaction_type Regulatory Interaction_phenotype ""


  • Interaction_type No_interaction Effector ""
  • Interaction_type No_interaction Effected ""
  • Interaction_type No_interaction Non_directional ""
  • Interaction_type No_interaction Interaction_RNAi ""
  • Interaction_type No_interaction Interaction_phenotype ""


  • Interaction_type Predicted_interaction Non_directional ""
  • Interaction_type Predicted_interaction Interaction_RNAi ""
  • Interaction_type Predicted_interaction Interaction_phenotype ""


  • Interaction_type Physical_interaction Effector ""
  • Interaction_type Physical_interaction Effected ""
  • Interaction_type Physical_interaction Interaction_RNAi ""
  • Interaction_type Physical_interaction Interaction_phenotype ""


  • Interaction_type Suppression Effector ""
  • Interaction_type Suppression Effected ""
  • Interaction_type Suppression Interaction_RNAi ""
  • Interaction_type Suppression Interaction_phenotype ""


  • Interaction_type Enhancement Effector ""
  • Interaction_type Enhancement Effected ""
  • Interaction_type Enhancement Interaction_RNAi ""
  • Interaction_type Enhancement Interaction_phenotype ""


  • Interaction_type Synthetic Non_directional ""
  • Interaction_type Synthetic Interaction_RNAi ""
  • Interaction_type Synthetic Interaction_phenotype ""


  • Interaction_type Epistasis Effector ""
  • Interaction_type Epistasis Effected ""
  • Interaction_type Epistasis Interaction_RNAi ""
  • Interaction_type Epistasis Interaction_phenotype ""


  • Interaction_type Mutual_enhancement Non_directional ""
  • Interaction_type Mutual_enhancement Interaction_RNAi ""
  • Interaction_type Mutual_enhancement Interaction_phenotype ""


  • Interaction_type Mutual_suppression Non_directional ""
  • Interaction_type Mutual_suppression Interaction_RNAi ""
  • Interaction_type Mutual_suppression Interaction_phenotype ""


  • Paper ""
  • Remark ""

== Some Notes for gene_gene_interaction ==

  • two large scale papers
    • WBPaper00027155 (Weiwei's science paper) has 23128 objects, starting from WBInteraction0008637 and ending at WBInteraction0050578 (blank ids in between)
    • WBPaper00031465 (Lee's Nature Genetics paper) has 375491 objects, starting from WBInteraction 0100001, ending at WBInteraction047451 (which is the largest WBInteraction id in acedb)