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 )