Session12 GENCODE: The reference human genome annotation for The ENCODE Project (Harrow et. al)

Preferred Infrastructure

oono@preferred.jp

Twitter:@delta2323_

2012/09/29

ENCODE@

GENCODE

GENCODE(1/1) Encyclopedia of genes and gene variants Identify all gene features in the human genome

Annotation of protein-coding gene, lncRNA loci and pseudogenes

Combination of computational analysis, manual annotation, and experimental validation.

713

(1/3 : GENCODE 13)

(2/3 : Transctipts, CDS(Fig.7))

(3/3 : Transctipts, CDS(Supplemental Figure 5))

GENCODE(1/3)

http://www.gencodegenes.org/releases/13.html

UIAPI (Supplemental Table 11)

UCSC genome brower

Ensembl genome browser

Ensembl BioMart (Perl/Ruby APIDB)

1000 Genome Project Consortium

International Cancer Genome Consortium

UCSC Genome Browser (2/3) http://genome-mirror.moma.ki.au.dk/cgi-bin/hgTracks

UCSC Genome Browser (3/3:Result)

http://genome-mirror.moma.ki.au.dk/cgi-bin/hgc?hgsid=192670&c=chr21&o=33032021&t=33041244&g=wgEncodeGencodeBasicV12&i=ENST00000470944.1

(1/2 : ) (Fig. 1)

(2/2 : ) (Supplementary Table1)

LocusBiotype, Status, Level

Biotype : protein-coding/lncRNA/(polymorphic)pseudogene Status : Known/Novel/Putative

Level : Level1:manually annotated and experimentally validated

Level2:manually annotated

Level3:automatically annotated

transcripts e.g. protein-coding locus

protein coding, NMD, NSD etc.

(1/1)

long non-coding RNA (lncRNA)

5058 lincRNA, 3214 antisense loci, 378 sense intronic loci, and 930 processed transcripts loci.

pseudogene PTENP1[Poliseno et al. 2010], DHFRL1[McEntee et al.

2011]

11224 pseudogene loci(=Level2)

7183 lociLevel1

934 loci(480(EST or cDNA)+454(HBM)) transcribed

(1/1)

100protein-coding loci

lincRNA(GENCODE42798lincRNA) NMDtranscript4

NMDmicroRNA[Bruno et al. 2011]

pseudogenepseudogene10000

de novo assemblytranscript

(Pacific Bioscience)Transcriptome annotation

(1/1)

GENCODE Ver.3~Ver.7

Quality Control System (Annotrack : Error Tracking System)

RT-PCR-seq PhyloCSFtranscript

putativetranscript

(Supplemental Table 5)

(Supplemental Figure 6)

Biomart Ruby Client (github)

pseudogenebiotype (Supplemental Table 1)