Subject:
SUMMARY points from pseudogene call on Thurs 21-Sept 11 AM EDT
Date:
Mon, 03 Oct 2005 00:42:23 -0400

Hi, here is the summary of the last call. -cheers, marK

==

** QUESTIONS

The pseudogene group is focusing on two questions:

- 1 - developing a consensus list of pseudogenes in the ENCODE
region. (This will involve understanding the various issues and
criteria used in assignment.)

- 2 - determining how many of the above have some activity in the
various encode functional genomics experiments

** TALLY

- Current tally as of 21-Sept call:

GIS: 46 processed pseudogenes
    (with strong evidence for transcription for at some of these)
Yale:  164 pseudogenes
Havana-Gencode: 167 pseudogenes
UCSC retrogenes: 146 not expressed

Union is 229 pseudogenes.
82 consensus intersection amongst all 4 groups.
45 non processed pseudogenes shared between Yale and Gencode.
102 not in the consensus

- Based on the call this has been slightly updated:

total 129 (80+12+37) pseudogenic regions to RT-PCR
80 pseudogenic regions agreed by GENCODE, YALE and UCSC initially
   (This includes some agreed on by GIS and a slight readjustment of the Gencode
    numbers.)
12 pseudogenic regions identified by YALE and UCSC initially, but
subsequently agreed by GENCODE.

37 non-processed pseudogenes agreed by GENCODE and YALE

We anticipate that they'll be further updates in relation to the data
freeze.

** RT-PCR+

The immediate plan for experimental analysis is that the consensus 129
should be given to Alexandre Reymond for RT PCR. This will perhaps be
given to Tom G. and AFFX people for further RACE experiments.

Here is Alex's summary of this:

<"

- 1. Robert will send us the 127 consensus sequence alignments of the
pseudogenes/parents and their respective mapping position (the latter being
important to pool wisely different RACEs)

- 2. We will design RACE primers (eventually two types, i.e. primers in region
that match exactly between pseudo/parent and specific ones)

- 3. We will perform the RACEs and teeze apart the results using Affymetrix
tiling
array chips with the help of Tom Gingeras.

We will discuss between us (Tom Gingeras, Philipp Kapranov, Stylianos
Antonarakis and myself) some technical aspects, e.g. how many RACEs to pool for
best efficiency and parcimonious use  of arrays, how many cDNA pool to test (we
have cDNA from the ENCODE cell lines and from 24 different human tissues,
etc...

">

** Interesting Cases (Havana ppt)

- Enr131: Deyou agreed with Adam and it is not a pgene

- Enr231: Looks interesting because it is called a pgene by Robert due
to presence of 3' UTR homology to gene.