Gene Set Summary
    Basis of gene set and why it's better than all the others.
    Estimates of total # of genes
Evolutionary Observations
    Fluidity of gene boundaries
	Genes transcribed separately or together
	Adding domains by:
	    Extending ends
	    Alternative promoters
	    Accretion of retroposons
	    Alternative splicing
    Gene duplication and loss
    	Transient expression after duplication
	Occassional incorperation
	    NM_003841 - an example of recent dupe that was
		transient in chimp but kept in human.
	Rate of loss in mouse & human using dog as outgroup.
	Selective pressure in duplicated areas
	# of genes in duplicated areas of various ages.
    Alt-splicing and selection
    	Conserved vs. nonconserved splicing.
	   Regulate splicing increases selective pressure.
	   Unregulated splicing similar to duplication, relaxes
	      selective pressure.
	Example of exon lost in human that is filled by many
	    different alt-exons
Protein domain analysis
    Pfam analysis
    GO-based pie chart of domains
    Rate of evolution of various domains.
Pervasiveness of alt-splicing
    Relationship of alt-splicing to alt-promoters
    # of isoforms vs. # of tissues expressed in
    # of isoforms sequences vs. expression levels
    Estimates of total # of transcripts
    Alt splicing and NMD
    Alt splicing inside the CDS
	Relationship of alt-splicing to domains.
	Estimates of total # of proteins including splice varients.
Analysis of noncoding genes
    Coding/nearcoding/antisense/noncoding distinctions.
    Conservation of noncoding transcripts.
    Secondary structure in noncoding transcripts.
    Artifacts and noncoding transcripts.
    Estimate of # of functional noncoding transcripts.
Where the genome goes wild
    Antibody clusters and their relationship to duplicons
    Things like antibody clusters
    	T Cell Receptors
	(If the new 2-3 minor AB clusters hold up mention here)
    Other duplicated areas and confetti regions
    The blast in the past - chromosome 19.
    Gene nurseries in the present.
Comparisons to other gene sets
    RefSeq
    Acembly
    Ensembl
    KG 2
Methods
    Overview
    Reference to txCdsPredict paper
    Reference to txGraph paper

Notes from Chuck:
	Microsatelights in genes.
	Indels etc in protein.