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VectorBase annotation metrics
Daniel Lawson
VectorBase-EBI, European Bioinformatics Institute,
Wellcome Trust Genome Campus, Hinxton UK
VectorBase BRC4 2006
1
Topics
• Annotation metrics
– Numbers (Gene numbers & xrefs)
– Data types (Availability & Integration)
• Annotation SOPs
– Genome specific
– Gene specific
– Gene build profile & prediction confidence
VectorBase BRC4 2006
2
AaegL1.1
AgamP3.3
Yeast
Worm
Fly
Human
Gene
Gene count
16,691
13,765
7,098
21,105
14,752
31,206
15,419 (92.4 %)
13,277 (96.5 %)
6,680
20,060
14,086
23,245
1,272 ( 7.6 %)
488 (3.5 %)
418
1,045
666
7,961
18,061
14,127
-
-
-
-
16,789 (93.0 %)
13,639 (96.5 %)
-
-
-
-
1,272 (7.0 %)
488 (3.5 %)
-
-
-
-
Manually reviewed
0 (0.0 %)
261 (1.9 %)
6,680
20,060
14,086
6,995
Community input
0 (0.0 %)
667 (4.9 %)
4,684
7,228
9,945
16,887
Combined
11,487 (74.5)
9,782 (73.7 %)
-
-
-
-
A.aegypti
n/a
8,907 (67.1 %)
2,202
4,416
7,991
6,590
A.gambiae
9,923 (54.9 %)
n/a
2,228
4,444
7,702
6,612
C.elegans
4,923 (29.5 %)
4,442 (33.4 %)
2,185
n/a
4,598
6,121
D.melanogaster
9,078 (50.3 %)
7,649 (57.6 %)
2,228
4,543
n/a
6,654
H.sapiens
5,510 (33.0 %)
5,046 (38.0 %)
2,326
4,473
5,109
n/a
S.cerevisiae
2,520 (15.1 %)
2,350 (17.7 %)
n/a
2,349
2,470
3,265
GO terms
9,335 (51.7 %)
7,601 (55.7 %)
4,176
11,334
10,226
17,000
EC numbers
2,950 (16.3 %)
2,230 (16.4 %)
4,103 *
5,240 *
4,009 *
13,245 *
11,536 (74.8 %)
9,869 (72.4 %)
4,611
14,730
10,475
18,199
Combined
12,350 (80.0 %)
7,557 (55.4 %)
-
-
-
-
cDNA/EST
9,270 (60.1 %)
7,557 (55.4 %)
-
-
-
-
microarray
9,143 (59.2 %)†
0 (0.0 %)‡
-
-
-
-
MPSS
3,984 (25.8 %)†
n/a
-
-
-
-
Protein-coding
other
Transcript
Transcript count
Protein-coding
other
Manual effort
Orthologs
Functional annotation
InterPro
Expression evidence
VectorBase BRC4 2006
3
Considerations
• Importance of calculating all metrics using similar
methodology from the same data set
• Metrics calculated from Ensembl using BioMart & raw
SQL queries.
• GO terms - many ways of calculating (InterPro2GO,
projection from Drosophila orthologs)
• No VectorBase capability to automatically assign EC
numbers
VectorBase BRC4 2006
4
AaegL1.1
AgamP3.3
Sequence
Yes
Download, search, visualization
Yes
Download, search, visualization
Polymorphisms
No
n/a
Yes
Search, visualization
Genetic maps
Yes
Not integrated
Yes
Visualization
Syntenic alignment
Yes
Visualization
Yes
Visualization
cDNAs & ESTs
Yes
Download, search, visualization
Yes
Download, search, visualization
SAGE tags
No
n/a
No
n/a
Microarrays
Yes
Visualization
Yes
Visualization
MPSS
Yes
Not integrated
No
n/a
Proteomics
No
n/a
No
n/a
Structures
No
n/a
No
n/a
Interactome data
No
n/a
No
n/a
Pathways
No
n/a
No
n/a
Orthology profiles
Yes
Visualization
Yes
Visualization
Essentiality data
No
n/a
No
n/a
VectorBase BRC4 2006
5
VB:SOP010
VectorBase gene prediction pipeline (SOP)
Blessed predictions
Manual annotations
Community submissions
VB:SOP007
Similarity predictions
VB:SOP002 & SOP003
Species-specific predictions
VB:SOP001
Canonical
Gene set
ncRNA predictions
VB:SOP008
Transcript based predictions
VB:SOP004
VectorBase BRC4 2006
Protein family HMMs
VB:SOP009
Ab initio gene predictions
VB:SOP005
6
Assignment of SOPs to VectorBase genes: AgamP3.3
SOP
No. genes
VB:SOP001
Confirmed
674
VB:SOP002
Protein-based with
transcript support
3765
VB:SOP003
Protein-based
4830
VB:SOP004
Transcript-based
2857
VB:SOP005
Supported ab initio
585
VB:SOP006
ab initio
0
VB:SOP007
Manual annotation
928
VectorBase BRC4 2006
7
Display of Metrics & SOPs
• Metrics
– VectorBase wiki
– Species-page containing the three tables available from the
VectorBase species homepage
– Expansion of documents relating to genomic resources (citations,
links to primary data where possible)
– Single collated table for BRC as separate download
• SOPs
– VectorBase wiki
– ‘Documents’ section of main site
VectorBase BRC4 2006
8
VectorBase BRC4 2006
9
Manual annotation progress
Protein-coding
gene No.
VectorBase
manual
Community
submission
Anopheles gambiae
AgamP3.3
13,277
current
261 ( 2.0 %)
667 ( 5.0 %)
2474 (18.6 %)
667* ( 5.0 %)
0 ( 0.0 %)
0 ( 0.0 %)
0 ( 0.0 %)
341 ( 2.2 %)
Aedes aegypti
AaegL1.1
15,419
current
VectorBase BRC4 2006
10
Merging gene sets
Gene set #1
Gene set #2
Reduce to single predictions per locus
Compare exon/intron structures
Identical
structures
Compatible
structures
Different
structures
Merge/Split
structures
Complex
No Map
Add isoform predictions based on EST/Peptide data
Canonical gene set
VectorBase BRC4 2006
11