Predicting FOXM1-Mediated Gene Regulation through the Analysis of Genome-Wide FOXM1 Binding Sites in MCF-7, K562, SK-N-SH, GM12878 and ECC-1 Cell Lines
Abstract
:1. Introduction
2. Results
2.1. Canonical and non-Canonical FOXM1 Binding Motifs
2.2. Functional Prediction of FOXM1 Target Genes
2.3. The association of FOXM1 and NFY in Regulating Cell-Cycle-Related Genes
2.4. FOXM1 and Super-Enhancers
2.5. FOXM1 as a Prognostic Marker for Various Types of Cancer
3. Discussion
4. Conclusions
5. Materials and Methods
5.1. ChIP-seq Data Analysis
5.2. Identification of Super-Enhancers
5.3. Motif Analysis
5.4. Gene Ontology, Protein–Protein Interaction-Based Network Analysis, and Visualization
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
FKH | Forkhead |
DBD | DNA binding domain |
CHR | Cell cycle genes homology region |
ChIP-seq | Chromatin immunoprecipitation followed by sequencing |
ENCODE | The encyclopedia of DNA elements |
GO | Gene ontology |
PPI | Protein–protein interaction |
SE | Super-enhancer |
BRCA | Breast invasive carcinoma |
KIRC | Kidney renal clear cell carcinoma |
KIRP | Kidney renal papillary cell carcinoma |
LGG | Brain lower grade glioma |
LIHC | Liver hepatocellular carcinoma |
LUAD | Lung adenocarcinoma |
PAAD | Pancreatic adenocarcinoma |
SKCM | Skin cutaneous melanoma |
UCEC | Uterine corpus endometrial carcinoma |
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Kang, K.; Choi, Y.; Kim, H.H.; Yoo, K.H.; Yu, S. Predicting FOXM1-Mediated Gene Regulation through the Analysis of Genome-Wide FOXM1 Binding Sites in MCF-7, K562, SK-N-SH, GM12878 and ECC-1 Cell Lines. Int. J. Mol. Sci. 2020, 21, 6141. https://doi.org/10.3390/ijms21176141
Kang K, Choi Y, Kim HH, Yoo KH, Yu S. Predicting FOXM1-Mediated Gene Regulation through the Analysis of Genome-Wide FOXM1 Binding Sites in MCF-7, K562, SK-N-SH, GM12878 and ECC-1 Cell Lines. International Journal of Molecular Sciences. 2020; 21(17):6141. https://doi.org/10.3390/ijms21176141
Chicago/Turabian StyleKang, Keunsoo, Yoonjung Choi, Hoo Hyun Kim, Kyung Hyun Yoo, and Sungryul Yu. 2020. "Predicting FOXM1-Mediated Gene Regulation through the Analysis of Genome-Wide FOXM1 Binding Sites in MCF-7, K562, SK-N-SH, GM12878 and ECC-1 Cell Lines" International Journal of Molecular Sciences 21, no. 17: 6141. https://doi.org/10.3390/ijms21176141