Table 1. Summary of Genes Used for in vivo CHIP Analysis.
| No. | Gene Symbol | Gene Name | GO Terms* | Array/qRT-PCR Fold Change | Genomic length (kb) | Transcript length (kb) | No. of Exons | Degree of Spt5 occupancy | Degree of RNAPII occupancy |
| Genes Up-regulated in 24 hpf fogsk8 Mutant Embryos | |||||||||
| 1 | gadd45b | Growth arrest and DNA-damage-inducible, beta | Stress response | 6.34/6.07 | 1.6 | 1.2 | 4 | ++++ | ++++ |
| 2 | fos | v-fos FBJ murine osteosarcoma viral oncogene | Transcription Factor | 5.68/8.44 | 2.1 | 1.7 | 4 | ++++ | ++++ |
| 3 | hsp70 | Heat shock protein 70 | Stress response | 5.6/2.32 | 3.4 | 2.3 | 2 | +++ | +++ |
| 4 | fst | Follistatin | Pattern specification | 2.25/2.07 | 5.5 | 3.4 | 5 | +++ | ++ |
| 5 | smo | Smoothened homolog | Pattern specification | 2.02/2.12 | 5.6 | 3.0 | 12 | +++ | ++++ |
| 6 | atf3 | Activating transcription factor 3 | Transcription Factor | 2/1.89 | 6.1 | 2.6 | 4 | +++ | ++ |
| 7 | tpbgl | Trophoblast glycoprotein-like | Receptor | 3.24/2.37 | 2.6 | 1.7 | 2 | ++ | +++ |
| 8 | foxd5 | Forkhead box D5 | Transcription Factor | 9.83/10.77 | 4.1 | 1.1 | 2 | + | + |
| 9 | bapx | Bagpipe homeobox 1/ NK3 homeobox 2 | Transcription Factor | 4.62/4.62 | 0.5 | 0.3 | 2 | − | − |
| 10 | zp2.4 | Zona pellucida glycoprotein 2.4 | Viral envelope | 3.74/6.02 | 1.8 | 1.3 | 8 | − | − |
| 11 | opn1sw2 | Opsin 1, short-wave-sensitive 2 | Signal transduction | 2.72/7.81 | 2.6 | 1.3 | 5 | − | − |
| Genes Down-regulated in 24 hpf fogsk8 Mutant Embryos | |||||||||
| 1 | lfng | Lunatic fringe homolog | Signaling | 3/3.68 | 9.4 | 2.9 | 8 | ++++ | ++++ |
| 2 | tpma | Alpha tropomyosin | Actin binding | 2.86/3.41 | 4.5 | 1.3 | 10 | +++ | +++ |
| 3 | a2bp1l | ataxin 2-binding protein 1-like | Nucleotide binding | 10.69/7.83 | 18.5 | 1.1 | 12 | ++ | ++ |
| 4 | ndrg1 | N-myc downstream regulated gene 1 | Cell differentiation | 6.04/8.47 | 19.9 | 2.3 | 16 | − | + |
| 5 | ldb3l | LIM domain binding 3 like | Protein binding | 3.64/3.44 | 39.3 | 1.6 | 12 | − | − |
| 6 | pvalb8 | Parvalbumin 8 | Calcium ion binding | 17.62/12.23 | 174.7 | 0.8 | 5 | − | − |
| 7 | atp1a1a.4 | ATPase, Na+/K+ transporting, alpha 1a.4 | Sodium\potassium ATPase | 3.37/62.85 | 7.5 | 3.2 | 22 | − | − |
| Genes Unchanged in 24 hpf fogsk8 Mutant Embryos | |||||||||
| 1 | bactin1 | Beta Actin 1 | Cytoskeleton | 1.26/−1.8 | 3.6 | 1.7 | 6 | +++ | ++++ |
| 2 | ccne | Cyclin E | Cell cycle | 1/1.87 | 9.8 | 2.0 | 12 | ++ | − |
| 3 | fkbp5 | FK506 binding protein 5 | Protein folding | 1/1.04 | 9.9 | 2.4 | 11 | − | − |
*
GO/MAPP program-suggested gene function.