Utr modeling part iii
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UTR Modeling Part III. Sam Gross Randy Brown. Old 5 ' UTR Model. Einit. Inter. Utr5. Prom. Esngl. Prom. ATG. Coding Exon. Inter. Utr5. New 5 ' UTR Model. Enc. Inc. Ep. Einit. Ea. Inter. Prom. Epa. Esngl. Prom. Epa. ATG. Coding Exon. Inter. Prom. Ep. Ea. ATG.

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UTR Modeling Part III

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Utr modeling part iii

UTR ModelingPart III

Sam Gross

Randy Brown


Old 5 utr model

Old 5' UTR Model

Einit

Inter

Utr5

Prom

Esngl

Prom

ATG

Coding Exon

Inter

Utr5


New 5 utr model

New 5' UTR Model

Enc

Inc

Ep

Einit

Ea

Inter

Prom

Epa

Esngl

Prom

Epa

ATG

Coding Exon

Inter

Prom

Ep

Ea

ATG

Coding Exon

Inter

Inc

Prom

Ep

Enc

Ea

ATG

Coding Exon

Inter

Inc

Inc


New data from dbtss 3 0

New Data From DBTSS 3.0

  • Extended RefSeq 5' UTR information by mapping full-length cDNAs from DBTSS using est2genome. 1500 genes in old training/testing set; new set has 6400 genes

  • Data set now large enough to move to directly-estimated length distributions for Ep, Epa, Ea, and Enc states


Utr modeling part iii

  • Separate UTR “coding” models for Ep/Epa and Ea/Enc

  • Tried UTR “coding” models of 3rd, 4th, and 5th order, with and without division by isochore. Best model was 4th order with isochore division.


Utr modeling part iii

  • Dual coding model (CpG-related/not CpG-related) for Ep, Epa, and Einit states was not very effective. Still working on modeling CpG islands.

  • Initial coding exon hexamer distribution depends more on whether the UTR is spliced or unspliced than whether the gene is associated with a CpG island or not

  • This suggests splitting the Einit state into two states, each with different coding parameters


Einits einitu 5 utr model

EinitS/EinitU 5' UTR Model

Enc

EinitS

Inc

Ep

Ea

Esngl

Inter

Prom

Epa

EinitU

Prom

Epa

ATG

EinitU

Inter

Prom

Ep

Ea

ATG

EinitS

Inter

Inc

Prom

Ep

Enc

Ea

ATG

EinitS

Inter

Inc

Inc


Future directions

Future Directions

  • Test performance of EinitS/EinitU model

  • Try directly-estimated length distributions for 5' UTR states

  • Conservation sequence models for 5' UTR states

  • CpG island model


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