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Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq.

Tran NT, Huang CH - Gene Regul Syst Bio (2014)

Bottom Line: Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer.We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions.These genes are not currently in the Ensemble gene database at NCBI.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.

ABSTRACT
Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we further identified highly expressed genes by H3K4me3 mark or by both H3K4me3 and H3K4me1 marks in mouse liver using ChIP-Seq and RNA-Seq. We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions. We also identified novel genes in RNA-Seq experiments for mouse liver and for mouse embryonic stem cells. These genes are not currently in the Ensemble gene database at NCBI.

No MeSH data available.


GO enrichment analysis for overlapping genes in Experiment 1 through Experiment 4. The GO enrichment level increases toward inner circle. The innermost circle has the highest GO enrichment level.
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f2-grsb-8-2014-033: GO enrichment analysis for overlapping genes in Experiment 1 through Experiment 4. The GO enrichment level increases toward inner circle. The innermost circle has the highest GO enrichment level.

Mentions: We performed the GOStat analysis for all overlapping genes found in Experiments 1–4.26 We observed all the GO enrichment by GO terms and P-values in ascending order. It showed that the GO enrichment for overlapping genes in Experiment 4 is the same as the GO enrichment for the overlapping genes in Experiment 2. The reason is that the overlapping genes found from these two experiments are almost identical and their quantities are very close to each other. In fact, they both have the same number of GO terms and P-values. Thus, their GO enrichments are similar. We also found the GO enrichment in Experiment 4 and the GO enrichment in Experiment 2 are contained in the GO enrichment of overlapping genes found in Experiment 1 using Filter 1. In addition, the GO enrichment in Experiment 1 using Filter 1 has more GO terms with bigger P-values. The GO enrichment in Experiment 1 using Filter 1 is contained in the GO enrichment of the overlapping genes found in Experiment 3 using Filter 3. Also, the GO enrichment in Experiment 3 using Filter 3 has more GO terms with larger P-values. Further, the GO enrichment in Experiment 3 using Filter 3 is contained in the GO enrichment of the overlapping genes found in Experiment 1 using Filter 3 and it is also contained in the GO enrichment of the overlapping genes found in Experiment 1 using Filter 2. However, the GO enrichment in Experiment 1 using Filter 3 and the GO enrichment in Experiment 1 using Filter 2 are identical but they have more GO terms with larger P-values. Figure 2 demonstrates the GO enrichment level for each experiment. To sum up, we observed that the more filters we applied, the less overlapping genes we obtained, but the level of GO enrichment went up because it contained highly expressed genes. This trend is expected if the filter criteria go higher.


Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq.

Tran NT, Huang CH - Gene Regul Syst Bio (2014)

GO enrichment analysis for overlapping genes in Experiment 1 through Experiment 4. The GO enrichment level increases toward inner circle. The innermost circle has the highest GO enrichment level.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3921077&req=5

f2-grsb-8-2014-033: GO enrichment analysis for overlapping genes in Experiment 1 through Experiment 4. The GO enrichment level increases toward inner circle. The innermost circle has the highest GO enrichment level.
Mentions: We performed the GOStat analysis for all overlapping genes found in Experiments 1–4.26 We observed all the GO enrichment by GO terms and P-values in ascending order. It showed that the GO enrichment for overlapping genes in Experiment 4 is the same as the GO enrichment for the overlapping genes in Experiment 2. The reason is that the overlapping genes found from these two experiments are almost identical and their quantities are very close to each other. In fact, they both have the same number of GO terms and P-values. Thus, their GO enrichments are similar. We also found the GO enrichment in Experiment 4 and the GO enrichment in Experiment 2 are contained in the GO enrichment of overlapping genes found in Experiment 1 using Filter 1. In addition, the GO enrichment in Experiment 1 using Filter 1 has more GO terms with bigger P-values. The GO enrichment in Experiment 1 using Filter 1 is contained in the GO enrichment of the overlapping genes found in Experiment 3 using Filter 3. Also, the GO enrichment in Experiment 3 using Filter 3 has more GO terms with larger P-values. Further, the GO enrichment in Experiment 3 using Filter 3 is contained in the GO enrichment of the overlapping genes found in Experiment 1 using Filter 3 and it is also contained in the GO enrichment of the overlapping genes found in Experiment 1 using Filter 2. However, the GO enrichment in Experiment 1 using Filter 3 and the GO enrichment in Experiment 1 using Filter 2 are identical but they have more GO terms with larger P-values. Figure 2 demonstrates the GO enrichment level for each experiment. To sum up, we observed that the more filters we applied, the less overlapping genes we obtained, but the level of GO enrichment went up because it contained highly expressed genes. This trend is expected if the filter criteria go higher.

Bottom Line: Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer.We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions.These genes are not currently in the Ensemble gene database at NCBI.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.

ABSTRACT
Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we further identified highly expressed genes by H3K4me3 mark or by both H3K4me3 and H3K4me1 marks in mouse liver using ChIP-Seq and RNA-Seq. We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions. We also identified novel genes in RNA-Seq experiments for mouse liver and for mouse embryonic stem cells. These genes are not currently in the Ensemble gene database at NCBI.

No MeSH data available.