## 3 Results
### Gse24850
#### 3.1.2 Comparisons with State-of-the-Art Methods  
Although the proposed method performed successfully, if other state-of-the-art methods perform similarly, the importance of the proposed method drastically decreases. To reject this possibility, various state-of-the-art methods were used to analyze the GSE24850 dataset. No state-of-the-art method had a comparative performance. MOSAiCS  
The first state-of-the-art method tested was MOSAiCS. Since MOSAiCS only accepts a pair of ChIP-seq and input datasets (i.e., a control), MOSAiCS was repeatedly applied to five pairs of ChIP-seq data (i.e., three saline and two cocaine samples) and one input profile. MOSAiCS identified 4367, 3648, 2096, 1985, and 5566 peak regions and 1833, 1599, 1136, 1018, and 2223 associated Entrez gene IDs. Finally, 994, 851, 567, 532, and 1184 gene symbols were identified. Next, these five sets of genes were uploaded to Enrichr one by one and the number of histone modifications that were significantly enriched in the \"Epigenomics Roadmap HM ChIP-seq\" category of Enrichr was determined. \begin{table}
\begin{tabular}{l c c c} \hline \hline
**Term** & **Overlap** & \(p\)**-Value** & **Adjusted \(p\)-Value** \\ \hline H3K9 me3 Brain Mid Frontal Lobe & 22/217 & \(2.02\times 10^{-6}\) & \(7.45\times 10^{-4}\) \\ H3K9 me3 Brain Inferior Temporal Lobe & 18/170 & \(9.31\times 10^{-6}\) & \(1.72\times 10^{-3}\) \\ H3K9 me3 CD4 Naive Primary Cells & 10/64 & \(3.39\times 10^{-5}\) & \(4.17\times 10^{-3}\) \\ H3K9 me3 Brain Anterior Caudate & 15/141 & \(4.82\times 10^{-5}\) & \(4.45\times 10^{-3}\) \\ H3K9 me3 IMR90 & 45/814 & \(2.82\times 10^{-4}\) & \(2.08\times 10^{-2}\) \\ H3K9 me3 Brain Hippocampus Middle & 15/170 & \(3.90\times 10^{-4}\) & \(2.40\times 10^{-2}\) \\ H3K9 me3 Stomach Smooth Muscle & 17/217 & \(6.56\times 10^{-4}\) & \(3.33\times 10^{-2}\) \\ H3K9 me3 Colon Smooth Muscle & 10/92 & \(7.24\times 10^{-4}\) & \(3.33\times 10^{-2}\) \\ H3K9 me3 CD8 Naive Primary Cells & 11/110 & \(8.11\times 10^{-4}\) & \(3.33\times 10^{-2}\) \\ H3K9 me3 Brain Cingulate Gyrus & 11/115 & \(1.17\times 10^{-3}\) & \(4.33\times 10^{-2}\) \\ \hline \hline \end{tabular}
\end{table} 
Table 3: Enriched histone modification in the “Epigenomics Roadmap HM ChIP-seq” category of Enrichr for the GSE24850 dataset (H3K9 me3). Figure 2: Histogram of \(1-P_{i}\) computed using the proposed method for the GSE24850 dataset (H3K9 me3). Table 4 shows the performance of MOSAiCS, which identifies at most only three significantly enriched histone modifications, of which two, at most, are H3K9 me3 modifications. Since the proposed method identified as many as 10 enriched histone modifications, all of which are H3K9 me3 modifications, the proposed method outperforms MOSAiCS. DFilter  
The next state-of-the-art method tested was DFilter, which was also applied to the five pairs of data. DFilter identified 25,080, 22,863, 21,371, 23,811, and 23,369 peak regions and 6286, 5721, 5407, 5987, and 5903 Entrez gene IDs, of which 2621, 2524, 2499, 2631, and 2544 gene symbols were associated with each of the five pairs. These sets of gene symbols were uploaded to Enrichr and no enriched H3K9 me3 modifications were observed (Table 4). Thus, the proposed method outperforms DFilter. F-Seq2  
The F-Seq2 method could not be performed with the available computer memory. Therefore, we could not compare the performance of F-Seq2 to the proposed method. HOMER  
The next state-of-the-art method was HOMER, which has been used in the ENCODE project and has been used for recent reports [35]. HOMER has the capability to compare five input profiles directly with five H3K9 me3 profiles. Using this capability, HOMER identified 114,727 peak regions, 6771 associated Entrez genes, and 6747 gene symbols, which were uploaded to Enrichr. Unfortunately, Enrichr did not identify enriched regions of H3K9 me3 modifications (Table 4). RSEG  
The last comparison was with the state-of-the-art method RSEG, which resulted in a core dump, although no compile errors were detected.