Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data

Table 2 Our result is more biologically meaningful than Hu et al.’s and Jiang et al.’s results

Test (with FDR = 0.05)	Our result vs. Hu et al.’s result	Our result vs. Jiang et al.’s result
Functional enrichment	Our result has an equal or higher enrichment score than Hu et al.’s result in 83% (93/112) of the cases.	Our result has an equal or higher enrichment score than Jiang et al.’s result in 83% (29/35) of the cases.
Expression coherence	Of the 112 TFs, 86% (96/112) show significantly higher expression coherence in our result, compared with only 2% (2/112) in Hu et al.’s result.	Of the 35 TFs, 49% (17/35) show significantly higher expression coherence in our result, compared with only 31% (11/35) in Jiang et al.’s result.
The prevalence of protein-protein interactions	Of the 112 TFs, 82% (92/112) are enriched for membership to a protein-protein interaction module in our result, compared with only 38% (43/112) in Hu et al.’s result.	Of the 35 TFs, 91% (32/35) are enriched for membership to a protein-protein interaction module in our result, compared with only 31% (11/35) in Jiang et al.’s result.

To show that our result is more biologically meaningful than Hu et al.’s and Jiang et al.’s results, we assessed the functional enrichment, the expression coherence, and the prevalence of protein-protein interactions. Our result outperforms their results across all measures. Note that the comparison between our result and Jiang et al.’s result was performed on 35 TFs since only the TF knockout targets of these 35 TFs were reported in Jiang et al.’s study.

ISSN: 1752-0509