Table 3. Genes found in both RNA-Seq and RIP-Seq, sorted alphabetically.
The seven protein-coding genes identified as significant based on RIP-Seq and RNA-Seq are given. For RIP-Seq, the total number of significant ‘hits’ (binding events) per gene are reported, counted across two independent RIP experiments. Fold denotes the minimum fold change observed across all of the hits, where fold change is expressed as (HuR/IgG), and q denotes the maximum q-value (false discovery rate value based on method of Benjamini-Hochberg) from testing for HuR binding to RNA. Location of binding overlaps the annotated gene unless otherwise noted. For RNA-Seq, fold denotes change (HuR KO/CTL).
| RIP-Seq | RNA-Seq | |||||||
|---|---|---|---|---|---|---|---|---|
| Gene ID | Symbol | Name | Fold ≥ | q | Hits | AveExpr | q | Fold |
| 12326 | Camk4 | calcium/calmodulin-dependent protein kinase IV | 637 | <1E-68 | 2 | 7.40 | .060 | 0.845 |
| 16423 | Cd47 | CD47 antigen (Rh-related antigen, integrin-associated signal transducer) | 51 | <1E-99 | 5 | 8.71 | .077 | 1.181 |
| 15568 | Elavl1 | ELAV (embryonic lethal, abnormal vision)-like 1 (Hu antigen R) | 159 | <1E-99 | 6 | 7.25 | .002 | 1.316 |
| 67698 | Fam174a* | family with sequence similarity 174, member A | 169 | <1E-99 | 4 | 4.70 | .111 | 1.111 |
| 18286 | Odf2 | outer dense fiber of sperm tails 2 | 149 | <1E-99 | 5 | 7.46 | .041 | 0.864 |
| 320554 | Tcp11l1* | t-complex 11 like 1 | 146 | <1E-99 | 2 | 0.49 | .073 | 1.632 |
| 106205 | Zc3h7a | zinc finger CCCH type containing 7 A | 31 | <1E-99 | 2 | 7.59 | .002 | 1.308 |
*Denotes the nearest annotated gene to the discovered binding site, rather than an overlapping annotated gene.