1. Modeling Functional Genomics Datasets CVM889-101
Lesson 7
25 June 2007 Fiona McCarthy

2. Functional genomics modeling I:
Lesson 7 Outline
Functional genomics modeling I:
a eukaryotic example

3. identified 5,198 proteins from chicken bursa
1,753 were B cell specific
1,972 were stroma specific
1,473 (28%) were shared between the two
identified 114 transcription factors (TFs)
42 of the bursal B cell TFs have not been reported before in any B cells
modeled Programmed Cell Death (PCD), cell differentiation and proliferation, and transcriptional activation
confirmed the in vivo expression of 4,006 “predicted”, and 6,623 ab initio, ORFs

4. Introduction
cellular processes in complex eukaryotes do not occur in isolation, but are directed by soluble factors and interactions between cells.
understanding the biology of higher eukaryotes requires progressing to whole organ proteomics.
used differential detergent fractionation-multidimensional protein identification technology (DDF-MudPIT) to model the bursal proteome.

5. The Chicken Bursa Proteome
extended DDF-MudPIT by isolating 577 membrane proteins, 11.3% of which contain 7–24 transmembrane domains
only 28.3% of proteins were common to both B cells and stroma
manually assigned GO terms to the previously unannotated chicken proteins that we identified
our manual annotations results in an approximately 20% increase number of GO associations for chicken

6. DDF-MudPIT: capturing the proteome

7. Nuclear Proteins
Nuclear proteins are the key regulators of cell function
identified 114 TFs in total
only 10 are previously reported in bursal B cells
54 have never been described in hematopoietic tissues in any species
Histone proteins and histone modifications regulate TF access to promoters, and thus HMEs regulate transcription indirectly
B cell-specific histone variants that we identified are transcriptional repressors not transcriptional activators
Couldn’t measure modifications in complex mixture
instead quantified HMEs to assess differences
in transcriptional activation

9. identified 114 TFs

11. The Chicken Bursa
Site of B cell development and initial differentiation
Expect to see:
Programmed Cell Death (PCD)
Cell differentiation
Cell proliferation
biological process

20. Modeling Your Data What do you expect from your system?
What do you see in your system?
What is missing that you expect to see?
What is there that you don’t expect to see?