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Exon skipping/inclusion

Exon skipping/inclusion. Alternative 3 ’ splice sites. Alternative 5 ’ splice sites. Mutual exon exclusion. Intron retention. 5 ’ ss. Branch Point. 3 ’ ss. exon1. exon2. GU. A. AG. exon1. exon2. GU. A. AG. U2. U1. UG. exon1. U1. U4/U6. U5. U2. A. exon2. AG. U4/U6.

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Exon skipping/inclusion

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  1. Exon skipping/inclusion Alternative 3’ splice sites Alternative 5’ splice sites Mutual exon exclusion Intron retention

  2. 5’ss Branch Point 3’ss exon1 exon2 GU A AG exon1 exon2 GU A AG U2 U1 UG exon1 U1 U4/U6 U5 U2 A exon2 AG U4/U6 exon1 U2 U5 exon1 exon2 exon2 A AG (A) RNA splicing by spliceosome

  3. (A) (B) (C) (D) SR protein or splicing activator U2AF Splicing repressor protein ESE or ESS Activation Inhibition

  4. Step 1 : Finding Frequent Itemset Ck: {Candidate k-sized itemset} Lk: {frequent k-sized itemset} L1 = {frequent 1-sized itemsets}; For (k = 2; Lk-1!= 0; k++} do begin Ck = apriori-gen (Lk-1); // New Candidates foreall transaction t D do begin Ci= substet (Ck, t); // Candidates contained in t forall candidates c  Ct do c.count ++; end Lk= {c  Ck | c.count > minsupp} end FrequentItems = ∪kLk; Step 2: Rule Generation Rules = rule-generate (FrequentItemsets)

  5. {} A E F C AB CG EF FG B AE EG AG BC BD BE BF BG 2-sized frequent itemsets {} {} B A A ABEG ABE BCG BDE BEF BEG BFG ABG AEG 3-sized frequent itemsets 4-sized frequent itemsets

  6. ABEG15 ABE125 ABG15 AEG15 BCG14 BDE13 BEF35 BEG15 BFG45 EFG5 AB125 AD1 AF1 BC14 BE1235 BG145 CE1 CG14 DF3 EF35 FG5 AC1 AE125 AG15 BD13 BF345 CD1 CF4 DE13 DG1 EG15 A125 B12345 C14 D13 E1235 F345 G145 {} Lattice of items. Grey node is not frequent

  7. 1-sized itemsets (support) A (0.6), B(1.0), C(0.4), D(0.4), E(0.8), F(0.6), G(0.6) 2-sized itemsets (support) {A,B}(0.6), {A,C}(0.2), {A,D}(0.2), {A,E}(0.6), {A,F}(0.2), {A,G}(0.4), {B,C}(0.4), {B,D}(0.4), {B,E}(0.8), {B,F}(0.6), {B,G}(0.6), {C,D}(0.2), {C,E}(0.2), {C,F}(0.2), {C,G}(0.4), {D,E}(0.4), {D,F}(0.2), {D,G}(0.2), {E,F}(0.4),{E,G}(0.4), {F,G}(0.4) 3-sized itemsets (support) {A,B,E}(0.6), {A,B,G}(0.4), {A,E,G}(0.4), {B,C,G}(0.4), {B,D,E}(0.4), {B,E,F}(0.4), {B,E,G}(0.4), {B,F,G}(0.4), {E,F,G}(0.2) 4-sized itemsets (support) {A,B,E,G}(0.4) (A) Sample DB (B) Finding frequent itemsets

  8. {} A:3 B:2 Item Link B:3 D:1 C:1 A B C:1 E:1 F:1 C D E:2 E F:1 G:1 D:1 F G F:1 E:1 G:1 G:1 FP-tree of items.

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