simpIntLists Package May 20, 2021 R topics documented: simpIntLists-package . .1 ArabidopsisBioGRIDInteractionEntrezId . .4 ArabidopsisBioGRIDInteractionOfficial . .6 ArabidopsisBioGRIDInteractionUniqueId . .7 C.ElegansBioGRIDInteractionEntrezId . .9 C.ElegansBioGRIDInteractionOfficial . 11 C.ElegansBioGRIDInteractionUniqueId . 13 findInteractionList . 14 FruitFlyBioGRIDInteractionEntrezId . 16 FruitFlyBioGRIDInteractionOfficial . 18 FruitFlyBioGRIDInteractionUniqueId . 19 HumanBioGRIDInteractionEntrezId . 21 HumanBioGRIDInteractionOfficial . 22 HumanBioGRIDInteractionUniqueId . 23 MouseBioGRIDInteractionEntrezId . 24 MouseBioGRIDInteractionOfficial . 25 MouseBioGRIDInteractionUniqueId . 27 S.PombeBioGRIDInteractionEntrezId . 28 S.PombeBioGRIDInteractionOfficial . 30 S.PombeBioGRIDInteractionUniqueId . 33 YeastBioGRIDInteractionEntrezId . 35 YeastBioGRIDInteractionOfficial . 38 YeastBioGRIDInteractionUniqueId . 41 Index 46 simpIntLists-package The package contains BioGRID interactions for various organ- isms in a simple format Description The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. 1 2 simpIntLists-package Details simpIntLists-package 3 Package: simpIntLists Type: Package Version: 1.0 Date: 2011-01-18 License: GPL version 2 or newer LazyLoad: yes Author(s) Kircicegi KORKMAZ, Volkan ATALAY, Rengul CETIN ATALAY Maintainer: Kircicegi KORKMAZ <[email protected]> References Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1; 34:D535-9 Examples > library(simpIntLists) > i<-findInteractionList("arabidopsis", "EntrezId") > i[1:5] [[1]] [[1]]$name [1] 828230 [[1]]$interactors [1] 832208 821860 5888 842783 834532 [[2]] [[2]]$name [1] 832208 [[2]]$interactors [1] 828230 821455 852713 831710 821860 5888 11144 [[3]] [[3]]$name [1] 821860 [[3]]$interactors [1] 828230 831710 832208 [[4]] [[4]]$name [1] 836259 4 ArabidopsisBioGRIDInteractionEntrezId [[4]]$interactors [1] 818903 825075 836259 819292 835842 816408 843133 836132 837479 819311 [11] 825382 816538 839341 819296 838883 832518 821807 822061 [[5]] [[5]]$name [1] 818903 [[5]]$interactors [1] 836259 834983 836248 837479 814686 825075 816394 837483 839300 821251 > data(ArabidopsisBioGRIDInteractionUniqueId) > ArabidopsisBioGRIDInteractionUniqueId[30:32] [[1]] [[1]]$name [1] "At2g18790" [[1]]$interactors [1] "At5g57360" "At1g09530" "At1g09570" "At2g25930" "At3g59060" "At5g02810" [7] "At4g17230" "At5g49230" "At5g59560" "At2g02950" "At5g61270" "At1g76500" [13] "At1g10470" "At1g04400" "At2g18790" "At5g63310" "At2g20180" "At2g43010" [19] "At5g35840" "At4g16250" "At4g18130" "At2g32950" "At1g22280" "At1g04240" [25] "At1g52240" [[2]] [[2]]$name [1] "At1g09530" [[2]]$interactors [1] "At2g18790" "At5g61380" "At3g59060" "At5g02810" "At5g61270" "At2g43010" [7] "At2g01570" "At1g09570" "At1g02340" "At1g14920" "At1g66350" "At3g03450" [13] "At5g17490" "At1g09530" [[3]] [[3]]$name [1] "At2g46970" [[3]]$interactors [1] "At5g61380" ArabidopsisBioGRIDInteractionEntrezId BioGRID interactions for thale cress (Arabidopsis thaliana), en- trez ids are used as identifiers ArabidopsisBioGRIDInteractionEntrezId 5 Description This data set contains a list of interactions for thale cress (Arabidopsis thaliana). The interactions are taken from BioGRID version 3.1.72, January 2011 release. For gene/protein entries, Entrez ids are used. Usage data(ArabidopsisBioGRIDInteractionEntrezId) Format The format is: List of 2118 A list containing the interactions. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. example: $ :List of 2 ..$ name : int 828230 ..$ interactors: int [1:12] 832208 821860 821860 832208 832208 821860 832208 5888 842783 834532 ... Source http://thebiogrid.org/download.php References Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1; 34:D535-9 Examples > data(ArabidopsisBioGRIDInteractionEntrezId) > ArabidopsisBioGRIDInteractionEntrezId[1:5] [[1]] [[1]]$name [1] 828230 [[1]]$interactors [1] 832208 821860 5888 842783 834532 [[2]] [[2]]$name [1] 832208 [[2]]$interactors [1] 828230 821455 852713 831710 821860 5888 11144 [[3]] [[3]]$name [1] 821860 [[3]]$interactors [1] 828230 831710 832208 6 ArabidopsisBioGRIDInteractionOfficial [[4]] [[4]]$name [1] 836259 [[4]]$interactors [1] 818903 825075 836259 819292 835842 816408 843133 836132 837479 819311 [11] 825382 816538 839341 819296 838883 832518 821807 822061 [[5]] [[5]]$name [1] 818903 [[5]]$interactors [1] 836259 834983 836248 837479 814686 825075 816394 837483 839300 821251 ArabidopsisBioGRIDInteractionOfficial BioGRID interactions for thale cress (Arabidopsis thaliana), of- ficial names are used as identifiers Description This data set contains a list of interactions for thale cress (Arabidopsis thaliana). The interactions are taken from BioGRID version 3.1.72, January 2011 release. For gene/protein entries, official names are used. Usage data(ArabidopsisBioGRIDInteractionOfficial) Format The format is: List of 2109 A list containing the interactions. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. example: $ :List of 2 ..$ name : chr "BRCA2(IV)" ..$ interactors: chr [1:12] "ATRAD51" "DMC1" "DMC1" "ATRAD51" ... Source http://thebiogrid.org/download.php References Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1; 34:D535-9 ArabidopsisBioGRIDInteractionUniqueId 7 Examples > data(ArabidopsisBioGRIDInteractionOfficial) > ArabidopsisBioGRIDInteractionOfficial[1:5] [[1]] [[1]]$name [1] "BRCA2(IV)" [[1]]$interactors [1] "ATRAD51" "DMC1" "RAD51" "ATDSS1(I)" "ATDSS1(V)" [[2]] [[2]]$name [1] "ATRAD51" [[2]]$interactors [1] "BRCA2(IV)" "ATRAD54" "RAD54" "BRCA2B" "DMC1" "RAD51" [[3]] [[3]]$name [1] "DMC1" [[3]]$interactors [1] "BRCA2(IV)" "BRCA2B" "ATRAD51" [[4]] [[4]]$name [1] "TOC1" [[4]]$interactors [1] "PIF4" "PIL6" "TOC1" "APRR9" "ZTL" "LKP2" "FKF1" "APRR3" "PIF3" [10] "PIL1" "PIL2" "PIL5" "LHY" "CCA1" "GI" "APRR5" "TIC" "ABI3" [[5]] [[5]]$name [1] "PIF4" [[5]]$interactors [1] "TOC1" "HRB1" "PIF7" "PIF3" "RGA1" "PIL6" "PHYB" "PHYA" "HFR1" "RGL2" ArabidopsisBioGRIDInteractionUniqueId BioGRID interactions for thale cress (Arabidopsis thaliana), unique ids are used as identifiers 8 ArabidopsisBioGRIDInteractionUniqueId Description This data set contains a list of interactions for thale cress (Arabidopsis thaliana). The interactions are taken from BioGRID version 3.1.72, January 2011 release. For gene/protein entries, unique ids (systematic names) are used. Usage data(ArabidopsisBioGRIDInteractionUniqueId) Format The format is: List of 2106 A list containing the interactions. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. example: $ :List of 2 ..$ name : chr "At4g00020" ..$ interactors: chr [1:12] "At5g20850" "At3g22880" "At3g22880" "At5g20850" ... Source http://thebiogrid.org/download.php References Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1; 34:D535-9 Examples > data(ArabidopsisBioGRIDInteractionUniqueId) > ArabidopsisBioGRIDInteractionUniqueId[1:5] [[1]] [[1]]$name [1] "At4g00020" [[1]]$interactors [1] "At5g20850" "At3g22880" "At1g64750" "At5g45010" [[2]] [[2]]$name [1] "At5g20850" [[2]]$interactors [1] "At4g00020" "At3g19210" "YGL163C" "At5g01630" "At3g22880" [6] "RP1-199H16.4" [[3]] [[3]]$name [1] "At3g22880" [[3]]$interactors [1] "At4g00020" "At5g01630" "At5g20850" C.ElegansBioGRIDInteractionEntrezId 9 [[4]] [[4]]$name [1] "At5g61380" [[4]]$interactors [1] "At2g43010" "At3g59060" "At5g61380" "At2g46790" "At5g57360" "At2g18915" [7] "At1g68050" "At5g60100" "At1g09530" "At2g46970" "At3g62090" "At2g20180" [13] "At1g01060" "At2g46830" "At1g22770" "At5g24470" "At3g22380" "At3g24650" [[5]] [[5]]$name [1] "At2g43010" [[5]]$interactors [1] "At5g61380" "At5g49230" "At5g61270" "At1g09530" "At2g01570" "At3g59060" [7] "At2g18790" "At1g09570" "At1g02340" "At3g03450" C.ElegansBioGRIDInteractionEntrezId BioGRID interactions for C.elegans (Caenorhabditis elegans), entrez ids are used as identifiers Description This data set contains a list of interactions for C.elegans (Caenorhabditis elegans). The interactions are taken from BioGRID version 3.1.72, January 2011 release. For gene/protein entries, Entrez ids are used. Usage data(C.ElegansBioGRIDInteractionEntrezId) Format The format is: List of 3573 A list containing the interactions. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. example: $ :List of 2 ..$ name : int 177286 ..$ interactors: int [1:4] 179791 178104 180982 178104 Source http://thebiogrid.org/download.php References Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1; 34:D535-9 10 C.ElegansBioGRIDInteractionEntrezId