Detection of Gene Interactions Based on Syntactic Relations

Algorithm 1

Example of LLL05 training data.

ID              11064201-3

sentence        In this mutant, expression of the spoIIG gene, whose transcription depends on both

             sigma(A) and the phosphorylated Spo0A protein, Spo0A∼P, a major transcription

             factor during early stages of sporulation, was greatly reduced at 43 degrees C.

words            word(0,“In,”0,1) word(1,“this,”3,6) word(2,“mutant,”8,13) word(3,“expression,”16,25)

             word(4,“of,”27,28) word(5,“the,”30,32) word(6,“spoIIG,”34,39) word(7,“gene,”41,44)

             word(8,“whose,”47,51) word(9,“transcription,”53,65) word(10,“depends,”67,73)

             word(11,“on,”75,76) word(12,“both,”78,81) word(13,“sigma(A),”83,90)

             word(14,“and,”92,94) word(15,“the,”96,98) word(16,“phosphorylated,”100,113)

             word(17,“Spo0A,”115,119) word(18,“protein,”121,127) word(19,“Spo0A∼P,”130,136)

             word(20,“a,”139,139) word(21,“major,”141,145) word(22,“transcription,”147,159)

             word(23,“factor,”161,166) word(24,“during,”168,173) word(25,“early,”175,179)

             word(26,“stages,”181,186) word(27,“of,”188,189) word(28,“sporulation,”191,201)

             word(29,“was,”204,206) word(30,“greatly,”208,214) word(31,“reduced,”216,222)

             word(32,“at,”224,225) word(33,“43,”227,228) word(34,“degrees,”230,236)

             word(35,“C,”238,238)

lemmas            lemma(0,“in”) lemma(1,“this”) lemma(2,“mutant”) lemma(3,“expression”)

             lemma(4,“of”) lemma(5,“the”) lemma(6,“spoIIG”) lemma(7,“gene”)

             lemma(8,“whose”) lemma(9,“transcription”) lemma(10,“depend”) lemma(11,“on”)

             lemma(12,“both”) lemma(13,“sigA”) lemma(14,“and”) lemma(15,“the”)

             lemma(16,“phosphorylated”) lemma(17,“spo0A”) lemma(18,“protein”)

             lemma(19,“Spo0A-P”) lemma(20,“a”) lemma(21,“major”) lemma(22,“transcription”)

             lemma(23,“factor”) lemma(24,“during”) lemma(25,“early”) lemma(26,“stage”)

             lemma(27,“of”) lemma(28,“sporulation”) lemma(29,“be”) lemma(30,“greatly”)

             lemma(31,“reduce”) lemma(32,“at”) lemma(33,“43”) lemma(34,“degree”)

             lemma(35,“C”)

syntactic_relations     relation(“subj:V_PASS-N,”31,3) relation(“mod_att:N-N,”7,6)

             relation(“mod_att:N-ADJ,”34,33) relation(“comp_during:N-N,”23,26)

             relation(“comp_of:N-N,”26,28) relation(“comp_on:V-N,”10,13)

             relation(“mod_att:N-N,”23,22) relation(“mod_att:N-ADJ,”18,16)

             relation(“mod:V_PASS-ADV,”31,30) relation(“mod_att:N-ADJ,”26,25)

             relation(“mod_att:N-ADJ,”23,21) relation(“mod_att:N-N,”18,17)

             relation(“comp_on:V-N,”10,18) relation(“appos,”19,23) relation(“subj:V-N,”10,9)

             relation(“appos,”18,19) relation(“comp_of:N-N,”3,7) relation(“comp_in:V-N,”31,2)

             relation(“comp_of:N-N,”9,7) relation(“comp_at:V_PASS-N,” 31,34)

             relation(“mod_att:N-N,”34,35)

agents         agent(13) agent(17)

targets          target(6)

genic_relations    genic_interaction(13,6) genic_interaction(17,6)