Regulatory Networks: Inferring functional relationships through Co-expression

E -ma il: k enth .br dz@ p u gG en e ex p ressio n d a ta n o t o n ly p rov id e u s in sig h ts in to d iscrete tra n scrip t a b u n -d a n ce o f sp eciÞ c g en es, b u t co n ta in cry p tic in fo rm a tio n th a t ca n n o t rea d ilyb e a ssessed w ith o u t in terp reta tio n . W e a g a in u sed d a ta o f th e p la n t A ra bid o p -sis th a lia n a a s o u r referen ce o rg a n ism , y et th e a n a ly sis p resen ted h erein ca nb e p erfo rm ed w ith a n y o rg a n ism w ith va rio u s d a ta so u rces. W ith in th e cell,in fo rm a tio n is tra n sd u ced v ia d i! eren t sig n a lin g ca sca d es a n d resu lts in d if-feren tia l g en e ex p ressio n resp o n ses. T h e in co m in g sig n a ls a re p erceiv ed fro mu p strea m sig n a lin g co m p o n en ts a n d h a n d ed to d ow n strea m m essen g ers th a tfu rth er d eliv er th e sig n a ls to e! ecto r p ro tein s w h ich ca n d irectly in s u en ce g en eex p ressio n . In m o st ca ses, w e ca n a ssu m e th a t p ro tein s, w h ich a re co n n ected too th er sig n a lin g co m p o n en ts w ith in su ch a reg u la to ry n etw o rk , ex h ib it sim ila rex p ressio n tra jecto ries. T h u s, w e ex tra cted a k n ow n fu n ctio n a l n etw o rk fro mlitera tu re a n d d em o n stra ted th a t it is p o ssib le to su p erim p o se m icro a rray ex -p ressio n d a ta o n to th e p a th w ay s. T h ereb y, w e co u ld fo llow th e in fo rm a tio n s owth ro u g h tim e res ected b y g en e ex p ressio n ch a n g es. T h is a llow ed u s to p red ict,w h eth er th e u p strea m sig n a l w a s tra n sm itted fro m k n ow n elem en ts co n ta in edin th e n etw o rk o r relay ed fro m o u tsid e co m p o n en ts. W e n ex t co n d u cted th ev ice v ersa a p p ro a ch a n d u sed la rg e sca le m icro a rray ex p ressio n d a ta to b u ild aco -ex p ressio n m a trix fo r a ll g en es p resen t o n th e a rray. F ro m th is, w e co m p u teda reg u la to ry n etw o rk , w h ich a llow ed u s to d ed u ce k n ow n a n d n ov el sig n a lin gp a th w ay s.K ey w o rd s: L a rg e sca le g en e ex p ressio n d a ta , co -ex p ressio n m a trix a n a ly sis,g en e reg u la to ry n etw o rk s, sig n a l tra n sd u ctio n p a th w ay, A tG en E x p ress