ENCODE Pseudogenes

Status on 6-Oct

We have a list of pseudogenes from four research groups. These pseudogenes are our starting point at this moment. We agree to add other pseudogenes later.

	GIS	HAVAVA	UCSC	Yale
GIS	46	42	45	39
HAVANA	42	165	104	132
UCSC	45	106	163	105
Yale	39	135	104	167

Roadmap of generating a concensus pseudogene annotation for the ENCODE regions

Step I -- filter the above lists to remove pseudogenes overlapping with current GENCODE coding exons /loci. Pseudogenes overlaping with introns or noncoding genes will be kept.

The HAVAVA/GENCODE annotations (exons only, version 02.1) used for filtering.
A list of pseudogenes overlapping with the above exons

Following are the filtered pseudogenes -- i.e., those overlapping with exons of Known_genes have been removed (except for HAVAVA list):

45 from GIS
185 from HAVANA/GENCODE --this is the version 02.1 pseudogene annotation (each entry is checked by Adam).
138 from UCSC
156 from Yale
A summary statistics of these filtered lists.

	GIS	HAVAVA	UCSC	Yale
GIS	45	44	42	38
HAVANA	44	185	113	144
UCSC	42	113	138	97
Yale	38	144	95	156

Step II -- take a union of the above pseudogenes. Where a pseudogenic region is annotated by more than one group, the boundary represents the smallest start and the largest end.

222 union pseudogenes.

Step III -- Assign a parent protein for each pseudogene in the union using a protein set from the UniProt. Pseudogenes without a matching protein are excluded.

The protein set -- SPROT TREMBL.

198 updated pseudogenes with their parent proteins identified.

Step IV -- re-align each pseudogene to its parent protein.

Resulting Alignments

Step V -- update consensus list of pseudogenes with boundaries derived from the alignment in Step IV.

The 198 concensus pseudogenes (differs from the above in terms of boundaries)

A table showing that these consensus pseudogenes intersect with 43 GIS, 177 HAVANA, 128 UCSC-retro, 146 UCSC-duplicated, 152 YALE pseudogenes (and 19 GENCODE exons).

Step VI -- The updated consensue list of pseudogenes with their assigned parent proteins and new classification (processed or non-processed).

Consensus pseudogenes with classification in ENCODE coordinates.

Consensus pseudogenes with classification in hg17 chromosome coordinates.

Alignments of consensus pseudogenes with their parent proteins.