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Gene predictor sensitivity and specificity, averaged for 12 Drosophila species

Table P1.  Gene predictors compared for sensitivity and specificity, averaged over all species.  Sensitivities for old (Eold) genes are determined by overlap of prediction exons with homology matches. Sensitivity for new genes (Enew.O and Enew.P) are determined from overlap with species gene expression exons (O) and phylogenetic assessed Dmel exons.  Specificity, Pv, is 1 ( predicted exons with none of the above evidence / total predicted exons). Ntr is number of predicted transcripts (distinct genes for some predictors).  Predictor classes (Ab-initio, Ab-initio with homology guidance, Homology mapping, Combiner) are discussed in the text.  The random predictor is a randomly sampled null hypothesis for predictions.

 

Ab-initio

Ab-initio + homology

 

Statistic

DL_SNP

RI_GID

BZ_CNA

A ave

BN_NSC

DL_SNO

NI_GNO

AH ave

Random

Eold

0.914

0.912

0.906

0.911

0.938

0.940

0.938

0.939

0.501

Enew.O

0.796

0.627

0.550

0.658

0.608

0.801

0.541

0.650

0.501

Enew.P

0.693

0.535

0.420

0.549

0.504

0.712

0.377

0.531

0.154

Pv

0.564

0.789

0.880

0.744

0.828

0.576

0.842

0.749

0.296

Ntr

34223

22418

15606

24082

18492

33278

19719

23830

0

 

 

 

 

 

 

 

 

 

 

 

Homology mapping

Combiner

Statistic

EE_CEX

EE_CGM

EE_CGW

OD_GPI

PH_GMP

H ave

EE_GLN

EE_GLR

C ave

Eold

0.901

0.908

0.891

0.844

0.879

0.885

0.968

0.951

0.960

Enew.O

0.177

0.175

0.173

0.156

0.202

0.177

0.663

0.607

0.635

Enew.P

0.111

0.070

0.073

0.075

0.062

0.078

0.525

0.442

0.484

Pv

0.945

0.958

0.969

0.949

0.948

0.954

0.827

0.860

0.844

Ntr

34429

18440

18817

12281

12237

19241

25501

19219

22360

 

Source: http://insects.eugenes.org/species/news/genome-summaries/genepredictions-compared.txt, D.G. Gilbert, Jan. 2007

 

Grouped Predictor Key:

A = pure ab-initio, AH= ab-initio with homology evidence, H = homology gene mapper, C = Combiner of other predictors

Group   ID     Predictor

A   DL_SNP: DGIL_SNP: SNAP predictor, no homology

A   RI_GID: RGUI_GID: geneid predictor

A   BZ_CNA: BATZ_CNA: CONTRAST predictor, no-homology set

AH  BN_NSC: BREN_NSC: N-SCAN predictor using homology evidence

AH  DL_SNO: DGIL_SNO: SNAP predictor using homology evidence

AH  NI_GNO: NCBI_GNO: GNOMON predictor using homology evidence

C   EE_GLN: EISE_GLN: Glean prediction combiner

C   EE_GLR: EISE_GLR: Glean recombined with higher weight to gene mappers

C   MD_JIG: UMD_JIG : Jigsaw prediction combiner

H   EE_CEX: EISE_CEX: Exonerate  (Dmel gene mapping)

H   EE_CGM: EISE_CGM: GeneMapper (Dmel gene mapping)

H   EE_CGW: EISE_CGW: GeneWise  (Dmel gene mapping)

H   OD_GPI: OXFD_GPI: Oxford gene pipeline (exonerate with Dmel gene mapping)

H   PH_GMP: PACH_GMP: GeneMapper (Dmel gene mapping)

                                   

Predictor Statistic:

Eold   = Sensitivity for "Old genes" (HSP_modDM, Dmel protein matches; about 40,000 exon locations/species)

Enew.O = Sensitivity for "New genes" (OLIV_EXP  - HSP_modDM; 5,000 to 10,000 exon locations/species)

Enew.P = Sensitivity for "New genes" (new Dmel exons by phylogenetic analysis; about 2,000 exon locations/species)

Pv     = Specificity to exons with evidence (around 50,000 locations have evidence, and 100,000 lack evidence/species. How many of the no evidence locations have predictions)

Sensitivity to Old/New genes = ( predicted.overlaps.evidence / total.evidence.exons)

Specificity =  1 - ( no_evidence.predicted.exons / total.predicted.exons )

 


Developed at the Genome Informatics Lab of Indiana University Biology Department