Theobroma cacao public gene set pub3i
08 March 2012, D. Gilbert, gilbertd at indiana edu
------------------------------------------------------------
Gene sets compared: Mars.v11 = this Theobroma cacao public gene set pub3i
  Cirad.v1 = Nature Genetics 2011, doi:10.1038/ng.736, http://www.nature.com/ng/journal/v43/n2/full/ng.736.html
  
Table E1. Cacao gene sets summary counts
  Statistic             Mars.v11   Cirad.v1
  ---------             -------    --------
  Locus count           29283       29484
   Same locus+CDS       13519       13709
   Same locus/different  8599       10646
   Unique locus          7337        4928
  Alternate transcripts 14920          0
  Poor  models          17244       17342
  Coding bases          35 Mb       34 Mb
  Exon bases            54 Mb       48 Mb
  ave protein size        319         286
  ave transcript size   2.3 Kb     1.5 Kb
  ----------------------------------------
  Locus = good gene loci, excluding those identified as
  transposons, fragments, or unsupported by gene evidence.
  Alternate transcripts of Mars gene set are all from EST/RNA
  transcript assemblies.  Poor models are not counted for coding
  and transcript sizes.  Same/unique loci for two gene sets
  are described in tables E4, E5.


Table E2. Cacao gene evidence recovered in gene sets
  Evidence    Nevd       Mars   Cirad
  ---------   ------     ----   ----
  Proteins    36Mb       76%    73%
  RNA exons   67Mb       57%    48% 
  Introns   161333       91%    82% 
  RNA genes  48404       67%    32%
  -----------------------------------
  Proteins and RNA exons are bases of evidence aligned to
  genome, and percent of gene models that match those.
  Introns are number of unique introns from multiple EST/RNA reads,
  and percent of gene models matching both splice ends.
  RNA genes are unique transcript assemblies, and
  percent gene models that align  >= 66% .


Table E3. Homology average for gene set proteins
  Tree gene set    TAIR10  Plant8
  -----------------------------------
    Cacao11_mars    632     549
    Cacao1_cirad    620     522
    Poplar          609
    Castor bean     591
    Grape           563
  -----------------------------------
  TAIR10=  average blastp bitscore to Arabidopsis, TAIR10, using
  10253 TAIR genes that are common best matches to all 5 gene sets.
  Plant8=  average blastp bitscore to best matching plant protein
  of 8 plant proteome sets.  Note that difference in gene sets of
  Cacao are in same range as difference among tree species gene sets,
  so that phylogeny and gene construction quality differences are 
  confounded.