Table 2. Differentially expressed well-known cancer and/or drug tolerance related TSGs, oncogenes, miRNAs and proteins after DAC treatment in breast cancer.
| 3D omics | Cancer relatedgenes/miRNAs/proteins | Up-regulated | Down-regulated | ||||
| HB2 | MDA-MB231 | SKBR3 | HB2 | MDA-MB231 | SKBR3 | ||
| Gene expression * | Tumor suppressor genes | CDKN1A [EL]GJA1 (CX43) [L] | CDKN1A [E]CST6 [E]PDCD4 [EL] | CDKN1A [E]BRCA1 [L]FLCN [E]RASSF1 [E] | DLGAP5 [L]FAT3 [EL]PTEN [L] | GJA1 (CX43) [L] | GJA1 (CX43) [EL]CADM1 [EL]CDKN1B [EL]ING4 [EL]STEAP3 [EL]PDCD4 [EL] |
| Oncogenes | CXCL1 [EL]CXCL2 [L]ETS1 [L]ETV7 [E]LCN2 [L]MAFF [EL]MAP3K8 [EL]PDGFB [L]RAB33B [L] | CXCL1 [EL]CXCL2 [EL]CXCL3 [EL]JUP [E]LCN2 [EL]RAB31 [EL] | BRAF [E]CXCL2 [EL]CXCL3 [E]KLF6 [EL]LCN2 [E]MYC [EL] | RAB15 [L] | MERTK [E]CXCR4 [EL] | ERBB2 [E]JUP [L]VAV1 [EL] | |
| Drug tolerance related genes | FGF2 [L]IL6 [EL]MDK [E]TNFSF10 [EL]VEGFA [L] | CSF2 [EL]IL6 [EL] | FGF2 [E]IL6 [EL]MDK [E]RAD51 [EL]SERPINB5 [EL]SFN [EL] | SERPINB5 [L] | COL1A1 [EL]VEGFA [E] | COL18A1 [EL]ERBB2 [E]TGFB1 [E]TNFSF10 [E]VEGFA [L] | |
| MiRNA expression ** | Tumor suppressor (oncosuppressor) miRNAs | miR-155 [EL]miR-126 [EL] | miR-193b [EL] | miR-155 [EL]miR-193b [E]miR-125b [EL] | miR-27b [EL]miR-210 [L]miR-15a [EL]miR-155 [EL] | miR-27b [EL]miR-210 [E]miR-15a [L]let-7f [L]let-7g [L]let-7i [E]miR-125a [E]miR-125b [E]miR-126 [L] | miR-27b [EL]miR-210 [EL]miR-15a [E]let-7f [EL]let-7g [EL]let-7i [EL] |
| OncomiRs | miR-494 [E]miR-378 [L] | miR-494 [E]miR-378 [E] | miR-27a [EL]miR-106b [EL]miR-130a [L]miR-378 [EL] | miR-27a [L]miR-106b [L]miR-21 [EL]miR-24-2 [E]miR-130a [L] | miR-27a [EL]miR-106b [EL]miR-21 [L]miR-24-2 [EL] | ||
| Drug tolerance related miRNAs | miR-638 [EL]miR-768 [EL] | miR-638 [EL]miR-34a [E] | miR-638 [EL]miR-768 [EL]miR-424 [E] | miR-28 [E]miR-181a [L]miR-27b [EL] | miR-28 [L]miR-181a [L]miR-27b [EL]miR-21 [EL]let-7i [E]miR-768 [L] | miR-28 [EL]miR-181a [E]miR-27b [EL]miR-21 [L]let-7i [EL]miR-17 [L] | |
| Protein expression *** | Proteins related to cell proliferation, neoplasms and angiogenesis | Arhgdib [E]Anxa2 [E]Tgf [E] | Gstm2 [EL]Lgals7 [EL]Pebp1 [EL]Sod2 [EL] | Cbx1 [EL] | Bat1 [EL]Pdia6 [EL]Rbbp7 [L]Ywhab [EL] | ||
| Proteins related to cell invasion and metastasis | P4hb [E] | Arhgdia [EL]Pebp1 [EL]Sod2 [EL] | Pdia6 [EL]Ywhaz [EL] | ||||
| Drug tolerance related proteins | P4hb [E] | Arhgdia [EL]Sod2 [EL] | Glo1 [EL] | Pdia6 [EL] | |||
The complete data include both early and late up- and down-regulations, P values and fold changes are presented in supplementary data.
*Dataset S2 & 5;
**Dataset S3 & 5;
***Dataset S4.
[E]: Early stage change (change after treatment and within passages 1 & 3); [L]: Late stage change (change within passages 5, 7 & 10);
[EL] Early and late change (change within passages 1-10).