0. eRNA expression ranking

eRNA expression is a widely used marker to characterize active enhancers. First, eRNAs expression profile in Pancreatic cancer were downloaded from TCeA Portal (https://bioinformatics.mdanderson.org/Supplements/Super_Enhancer/TCEA_website/). To elucidate the expression level of enhancer of interest relative to all enhancers, adjacent non-tumor samples were extracted. The eRNAs were then ranked according to their expression levels in these samples.

Results showed that the expression of the eRNA of interest was at a medium-to-high level overall.

1. Normal vs Tumor expression

Samples were divided into tumor and adjacent non-tumor samples. Statistical analysis was conducted to determine the difference of eRNA expression levels between the two groups.

2. Survival analysis

2.1 Total samples, median

Aberrant activation of enhancers is closely associated with occurrence, progression, and prognosis of numerous diseases. To evaluate whether the expression level of eRNA is correlated with the survival of Pancreatic cancer patients, clinical prognostic information for the corresponding samples was obtained from The Cancer Genome Atlas (TCGA). Samples were stratified into two groups based on median expression value of eRNA: high eRNA expression and low eRNA expression. Survival differences between two groups were statistically analyzed using log-rank test with the survival package (v.3.4.0) in R. A P value of less than 0.05 was considered statistically significant.

2.2 Filter out low expression samples, median

After filtering out samples with low expression levels (FPKM < 0.001), Samples were stratified into two groups based on median expression value of eRNA: high eRNA expression and low eRNA expression. Survival differences between two groups were statistically analyzed using log-rank test with the survival package (v.3.4.0) in R. A P value of less than 0.05 was considered statistically significant.

2.3 Filter out low expression samples, best cutoff

After filtering out samples with low expression levels (FPKM < 0.001), Samples were stratified into two groups based on optimal cutpoint determined by survminer. Survival differences between two groups were statistically analyzed using log-rank test with the survival package (v.3.4.0) in R. A P value of less than 0.05 was considered statistically significant.

2.4.1 BRCA1-proficient group (BRCA1 High expression)

eRNA expression profile of TCGA Pancreatic cancer cohort was downloaded from TCeA (https://bioinformatics.mdanderson.org/Supplements/Super_Enhancer/TCEA_website/). Patients were divided into two groups based on median BRCA1 expression. eRNA expression correlation with patients’ survival were analyzed in each group.

eRNA expression correlation with patients’ survival were analyzed in BRCA1-proficient samples. Statistical significance was assessed using log-rank test.

2.4.2 BRCA1-deficient group (BRCA1 Low expression)

eRNA expression correlation with patients’ survival were analyzed in BRCA1-deficient samples. Statistical significance was assessed using log-rank test.

3. Clinical correlations

To evaluate the correlation between eRNA expression and clinical characteristics, samples were grouped by age, gender, and different stages. The Wilcoxon test was used to assess the differences of eRNA expression levels between different groups.

4. Genomic features

Spearman correlation was employed to assess the associations between eRNA expression and genomic features such as tumor mutational burden (TMB), homologous recombination deficiency (HRD), and microsatellite instability (MSI).

Time cost

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