Gene Interaction

'links to relevant pages
Caltech documentation
Interaction

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Pipeline

semi-automatic curation with textpresso extracted sentences

• There are 2138 sentences (actually 2133 sentences) in the sourcefile /home/postgres/work/pgpopulation/genegeneinteraction/20091002-xiaodong/ggi_20091002
  • paper starts at WBPaper00028425, ends at WBPaper00035225

• .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

• 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 //WBGene, multiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
  • Effected Variation //WBGene, WBVar, multiontology, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar". use name server to map variation to gene, or the file Karen gave you to map variation to gene for variation OA.
  • Effected Transgene_Name //ontology
  • Effected Transgene_Gene // multi-ontology, ->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id.
  • Effector Gene //WBGene, multiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
  • Effector Variation //WBGene, WBVar, multiontology, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar". use name server to map variation to gene, or the file Karen gave you to map variation to gene for variation OA. **Effector Transgene_Name //ontology
  • Effectot Transgene_Gene // multi-ontology, ->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id.

• 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 ""

interaction objects source file

• there are 9242 interaction objects dumped from WS220 on Monday, 10/01/2010

• Juancarlos's parse results from this file:

/home/postgres/work/pgpopulation/interaction/20101004_xiaodong_start/out

There are two interactions in postgres, but not the .ace file : In postgres, no ace WBInteraction0008637 In postgres, no ace WBInteraction0008638//will be OA

There are 1290 interactions in .ace file not in postgres (so I imagine these are what we should read in ?)//these are RNAi based interaction objects, we want to include them in OA

There are >40000 interactions that have a ticket and are in neither .ace nor postgres.//these 398,619 interactions are from two large scale papers

Also there are interaction data in postgres without an interaction ID//will be assigned id from WBInteraction0500001.

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)