set E F was found higher expressed in
set,32 E2F7 was found higher expressed in ductal breast carcinoma and 8 and the Decreased mRNA Expression of E2F4 and 6 with
(fold change = 4.535), and, in The Cancer Genome Atlas data (Ta- the Improved Prognosis of Patients with Breast Cancer
ble 1), higher expressed E2F7 was found in invasive breast carcinoma We further explored the critical efficiency of E2Fs in the survival of
(fold change = 5.193), invasive ductal breast carcinoma (fold change = patients with breast cancer. Kaplan-Meier Plotter tools were used to
Figure 4. The Expression of E2Fs in Breast Cancer (IHC)
analyze the correlation between the mRNA levels of E2Fs and the survival of patients with breast cancer by using publicly available datasets (2015 version; http://kmplot.com/analysis/index.php? p=service&cancer= breast). The Kaplan-Meier curve and log rank test analyses revealed that SCH 58261 the increased E2F1–3, 5, 7, and 8 mRNA levels and the decreased E2F4 and 6 mRNA levels were significantly associated with the overall survival (OS), progression-free survival (FP), and post-progression survival (PPS) (p < 0.05) (Figure 5) of all of the patients with breast cancer. The patients with breast cancer with high mRNA levels of the E2F1–3, 5, 7, and 8 factors or low mRNA levels of E2F4 and 6 were predicted to have high OS, FP, and PPS.
Predicted Functions and Pathways of the Changes in E2F Factors and Their Frequently Altered Neighbor Genes in Patients with Breast Cancer
We analyzed the E2F alterations, correlations, and networks by using the cBioPortal online tool for breast invasive carcinoma (The Cancer Genome Atlas, Provisional; http://www.cbioportal.org/index.do? session_id=5b4c1773498eb8b3d566f7b8). E2Fs were altered in 1,098 samples of 1,105 patients with breast invasive carcinoma (97%). Two or more alterations were detected in almost 2/3 of the samples (737 samples) (Figure 6A). We also calculated the correla-tions of E2Fs with each other by analyzing their mRNA expressions (RNA sequencing [RNA-seq] version (v.)2 RSEM) via the cBioPortal online tool for breast invasive carcinoma (The Cancer Genome Atlas,
The functions of E2Fs and the genes significantly associated with E2F alterations were predicted by analyzing gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) in the Database for Annotation, Visualization and Integrated Discovery (DAVID) (https://david.ncifcrf.gov/summary.jsp). GO enrichment analysis predicted the functional roles of target host genes on the basis of three aspects, including biological processes, cellular components, and mo-lecular functions. We found that GO:0006351 (transcription, DNA-templated), GO:0006270 (DNA replication initiation), GO:0006260 (DNA replication), GO:0000082 (G1/S transition of mitotic cell cycle), GO:0051726 (regulation of cell cycle), and GO:0000122 (nega-tive regulation of transcription from RNA polymerase II promoter) were significantly regulated by the E2F alterations in breast adenocar-cinoma (Figure 7A). GO:0005667 (transcription factor complex) and GO:0016538 (cyclin-dependent protein serine/threonine kinase
Figure 5. The Prognostic Value of mRNA Level of E2F Factors in Breast Cancer Patients (Kaplan-Meier Plotter)
regulator activity) were also significantly controlled by these E2F alterations (Figures 7B and 7C). They are well-known genes associ-ated with the cell cycle.
KEGG analysis can define the pathways related to the functions of E2F alterations and the frequently altered neighbor genes; 15 path-ways related to the functions of E2F alterations in breast adenocarci-noma were found through KEGG analysis (Figure 8). Among these pathways, cfa04110:Cell cycle, cfa04350:TGF-beta signaling pathway, ptr05200:pathways in cancer, cfa04115:p53 signaling pathway, and cfa04310:Wnt signaling pathway were involved in the tumorigenesis and pathogenesis of breast adenocarcinoma (Figures 9A and 9B).