Bioinformatics Analysis of the Potentially Functional circRNA-miRNA-mRNA Network in Breast Cancer

The files for "Bioinformatics Analysis of the Potentially Functional circRNA-miRNA-mRNA Network in Breast Cancer" https://www.biorxiv.org/content/10.1101/2022.01.10.475557v1

Abstract Figure

Main Figures

Main figures can be found in "Main figures.pptx".

Tables:

Table 1: Essential characteristics of the three DECs. (Table_1.xlsx)

Table 2: Expression levels of detected miRNA and possible target genes. (Table_2.xlsx)

Supplementary Figures:

Supplementary figures can be found in "Supplementary -> Supplementary figures.pptx".

Supplementary Tables:

1- The details of the clinical data for each datasets can be found in Table S1 separately. (Supplementary -> Table S1.xlsx)

2- We observed that 149 circRNAs (94 of them were up-regulated and 55 were down-regulated given in Table S2) in GSE101124 and 993 circRNA (665 of them were up-regulated and 328 were down-regulated given in Table S3) in GSE182471 in BC tumor samples were differentially expressed, when compared to the control samples. (Supplementary -> Table S2 - S3.xlsx)

3- The overlapped up- and down-regulated circRNAs are given in Table S4 and Table S5 for each dataset separately. (Supplementary -> Table S4 - S5.xlsx)

4- As regards to the miRNAs, in TCGA dataset 133 miRNAs (66 of them were up-regulated and 67 were down-regulated) in BLBC samples, 114 miRNAs (65 up- and 49 down-regulated) in HER2-positive samples, 105 miRNAs (49 up- and 56 down-regulated) in LumA group, 133 miRNAs (69 up- and 64 down-regulated) in LumB group, and 78 miRNAs (41 up- and 37 down-regulated) in normal-like tumor group were differentially expressed, when compared to the control samples. The top 10 up- and down-regulated miRNAs are given in (Table S6) and 25 up-regulated (Table S7) and 17 down-regulated miRNAs (Table S8) were shared across all five PAM50 classes. In addition, the up- and down-regulated miRNAs are listed in Tables S9-S13 for each PAM50 subtype separately. Furthermore, in METABRIC dataset 69 miRNAs (34 of them were up-regulated and 35 were down-regulated) in BLBC samples, 66 miRNAs (31 up- and 35 down-regulated) in HER2-positive samples, 51 miRNAs (28 up- and 23 down-regulated) in LumA group, 70 miRNAs (31 up- and 39 down-regulated) in LumB group, and 31 miRNAs (17 up- and 14 down-regulated) in normal-like tumor group were differentially expressed, when compared to the control samples. The top 10 up- and down-regulated miRNAs are given in (Table S14) and 9 up-regulated (Table S15) and 10 down-regulated miRNAs (Table S16) were shared across all five PAM50 classes. In addition, the up- and down-regulated miRNAs are listed in Tables S17-21 for each PAM50 subtype separately. (Supplementary -> Table S6 - S21.xlsx)

5- The top 10 up-regulated and down-regulated genes in each PAM50 class compared to the control samples according to our established criteria are listed in Table S22. Among the up-regulated genes, 746 were shared (Table S23) across all five PAM50 classes, whereas 650 down-regulated genes were shared (Table S24) across all five PAM50 classes. Additionally, the up- and down-regulated gene lists are provided in Tables S25-S29 for each PAM50 subtype individually. (Supplementary -> Table S22 - S29.xlsx)

6- The significantly enriched KEGG pathways with a FDR < 0.05 according to ten hubgenes given in (Supplementary -> Table S30).