Gene Interaction

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'links to relevant pages
Caltech documentation
Interaction


Interaction Curation

Pipeline

semi-automatic curation with textpresso extracted sentences

  • There are 2138 sentences in the sourcefile /home/postgres/work/pgpopulation/genegeneinteraction/20091002-xiaodong/ggi_20091002
  • .ace dumper at /home/acedb/xiaodong/gene_gene_interaction/dump_ggi_ace.pl
      • go to the directory and do: ./dump_ggi_ace.pl > some_file.ace

Interaction Model

?Interaction   Evidence #Evidence
              Interactor    ?Gene    XREF Interaction    #Interactor_info
              Interaction_type    Genetic    #Interaction_info
                                  Regulatory    #Interaction_info
                                  No_interaction    #Interaction_info
                                  Predicted_interaction    #Interaction_info
                                  Physical_interaction    #Interaction_info
                                  Suppression    #Interaction_info
                                  Enhancement    #Interaction_info
                                  Synthetic    #Interaction_info
                                  Epistasis    #Interaction_info
                                  Mutual_enhancement    #Interaction_info
                                  Mutual_suppression    #Interaction_info
              Confidence          Confidence_level        UNIQUE Float
                                  P_value                 UNIQUE Float
                                  Log_likelihood_score    UNIQUE Float			           
              Paper          ?Paper XREF Interaction
              DB_info      Database ?Database ?Database_field ?Accession_number
              Remark      ?Text   #Evidence 


#Interactor_info    
                               Variation    ?Variation    XREF    Interactor
                   	        Transgene ?Transgene XREF   Interactor
                               Remark  ?Text   #Evidence    //info about the reagents that the model can't capture goes here (e.g. co_suppression, RNA_reagent, etc.)
#Interaction_info    
                    Interaction_RNAi ?RNAi XREF Interaction
                    Effector ?Gene //master, upstream
                    Effected ?Gene //subject, downstream
                    Non_directional ?Gene //e.g. synthetic interactions - Igor
                    Interaction_phenotype ?Phenotype XREF Interaction
                    Confidence    Confidence_level        UNIQUE Float
                                            P_value                  UNIQUE Float


#Interaction_type 
                 Genetic //directional and non_directional
                 Physical_interaction
                 Regulation
                 No_interaction
                 Synthetic//non_directional
                 Epistasis
                 Enhancement
                 Suppression
                 Predicted  //addition for WeiWei, non_direactional
                 Mutual_enhancement//non_directional
                 Mutual_suprression//non_directional
///////////////////////////////////////////////////////////////////////////////////

Gene_gene Interaction OA

OA interface

Tab1.png

  • 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//WBGene, WBVar, etc. Imultiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
    • Effector Gene/Variation/Transgene//WBGene, WBVar, etc. multiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors


Tab2.png

  • 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 WBInteraction0475491 (which is the largest WBInteraction id in acedb)