Background
Materials and methods
Data collection
DEGs identification
Cell culture, RNA extraction and quantitative PCR (qPCR)
GO and biological pathway enrichment analysis
PPI network construction and analysis
Validation of the hub genes
miRNA–hub gene network
Drug-hub gene interaction
Results
Identification of DEGs
DEGs | Genes name |
---|---|
Upregulated (120) | NCAPH, P3H4, COL3A1, GGH, ADAM12, NUP155, TPX2, CCNB1, SHCBP1, HMGB3, NETO2, MMP3, IGF2BP2, CENPE, ASPM, SOX4, SPAG5, ANP32E, FAP, TBC1D31, CDCA3, GINS1, ACTL6A, ATAD2, KPNA2, COL1A1, POSTN, BIRC5, STIL, UBE2C, KNTC1, FSCN1, FOXM1, CCNB2, PRC1, HSPBAP1, BORA, CDK1, CHEK1, LRP8, FZD2, CEP55, MINPP1, KIF18B, DNMT3B, TOP2A, FEN1, FANCI, RAD54L, CCNE2, NCAPD2, CDC6, SPC25, CST1, MCM2, MCM4 KIF18A, KIF15, APOBEC3B, AURKA, KIF14, HEY1, BUB1B, TIMELESS, DLGAP5, HJURP, RAD51AP1, AURKB, HDGFRP3, CKS1B, TIPIN, RNASEH2A, MKI67, DTL, RAD51, MEST, MARCKSL1, HMMR, COL5A2, KIF4A, NCAPG2, EXO1, RAD54B, CENPI, GMNN, FZD6, KIF2C, KIF20A, CBS, ORC6, SIX1, TYMS, MELK, CDC20, CENPN, CDH11, NDC80, HOXB7, CCNA2, GTSE1, CDKN3, BUB1, NCAPG, COL1A2, SLC16A1, LAPTM4B, MMP1, TRIP13, APOC1, NEK2, STMN1, CENPF, NUSAP1, EPCAM, CKS2, ISG15, ECT2, ITPR3, KIF23, RPL39L |
Downregulated (26) | HSPB8, CRYAB, COL14A1, CXCR2, CRIP2, HLF, ADIRF, AHNAK, RBPMS, FAM189A2, SORBS2, EMP1, FMO2, RRAD, EPS8L1 MEIS1, ADH1B, FAM107A, MXD1, GPX3, ABLIM3, EREG, MAFF, SSBP2, ABLIM1, P2RY14 |
Enrichment analysis and PPI network
Functional enrichment analysis of DEGs
PPI network construction and modules analysis
Genes | Degree | p-value |
---|---|---|
CDK1 | 80 | < 0.001 |
CCNB1 | 78 | < 0.001 |
TOP2A | 77 | < 0.001 |
CCNB2 | 76 | < 0.001 |
BUB1 | 76 | < 0.001 |
CCNA2 | 76 | < 0.001 |
NCAPG | 75 | < 0.001 |
AURKB | 75 | < 0.001 |
NDC80 | 74 | < 0.001 |
BUB1 | 74 | < 0.001 |
Genetic information and hub genes expression
miRNA–hub genes network
Drug-gene interaction
Number | Gene | Drug | Interaction types | Approved? | Scoresa | Ref. (PubMed ID) |
---|---|---|---|---|---|---|
1 | CDK1 | ELTROMBOPAG | Agonist | FDA | 1 | – |
2 | CDK1 | ROMIPLOSTIM | Agonist | FDA | 1 | – |
3 | TOP2A | DOXORUBICIN HYDROCHLORIDE | Inhibitor | FDA | 13 | – |
4 | TOP2A | TENIPOSIDE | Inhibitor | FDA | 12 | 8702194; 16271071; 17361331; 17514873; 11752352; 16480143; 9426516 |
5 | TOP2A | ETOPOSIDE | Inhibitor | FDA | 12 | 8823806; 9485461; 8870683; 9494516; 9426516 |
6 | TOP2A | VINCRISTINE | – | FDA | 10 | 9494516 |
7 | TOP2A | DOXORUBICIN | Inhibitor | FDA | 9 | – |
8 | TOP2A | NORFLOXACIN | Inhibitor | FDA | 6 | 11752352 |
9 | TOP2A | VALRUBICIN | Inhibitor | FDA | 6 | 11752352; 16019763 |
10 | TOP2A | LEVOFLOXACIN | Inhibitor | FDA | 4 | 11752352 |
11 | TOP2A | ENOXACIN | Inhibitor | FDA | 4 | 18471102; 11752352; 10089819 |
12 | TOP2A | ETOPOSIDE PHOSPHATE | – | FDA | 3 | – |
13 | TOP2A | PACLITAXEL | – | FDA | 2 | – |
14 | TOP2A | DAUNORUBICIN | Inhibitor | FDA | 2 | 9494516 |
15 | TOP2A | OFLOXACIN | Inhibitor | FDA | 2 | 2847647 |
16 | TOP2A | IDARUBICIN HYDROCHLORIDE | Inhibitor | FDA | 2 | – |
17 | TOP2A | PEFLOXACIN | Inhibitor | FDA | 2 | 11752352 |
18 | TOP2A | DAUNORUBICIN HYDROCHLORIDE | Inhibitor | FDA | 2 | – |
19 | TOP2A | MITOXANTRONE DIHYDROCHLORIDE | Inhibitor | FDA | 2 | – |
20 | TOP2A | AMSACRINE | Inhibitor | FDA | 2 | 1322791; 8823806; 10691026; 8519659; 8632768; 11006484; 11716434; 11752352; 11473732; 1311390 |
21 | TOP2A | PODOFILOX | Inhibitor | FDA | 2 | 16061385; 1334447; 10783066; 11752352; 1845848; 1331331 |
22 | TOP2A | DEXRAZOXANE | – | FDA | 2 | 12911317 |
23 | TOP2A | MITOXANTRONE | Inhibitor | FDA | 2 | 10451375; 11004693; 18687447; 11752352; 9631585; 9494516; 11278845; 9426516 |
24 | TOP2A | LOMEFLOXACIN | Inhibitor | FDA | 1 | 11752352 |
25 | TOP2A | EPIRUBICIN | Inhibitor | FDA | 1 | 14728934; 16234514; 17639997 |
26 | TOP2A | DACTINOMYCIN | – | FDA | 1 | 9494516 |
27 | TOP2A | DAUNORUBICIN CITRATE | Inhibitor | FDA | 1 | – |
28 | TOP2A | FINAFLOXACIN | Inhibitor | FDA | 1 | 25808831 |
29 | TOP2A | IDARUBICIN | – | FDA | 1 | – |
30 | TOP2A | HYDROQUINONE | – | FDA | 1 | 15833037 |
31 | CCNA2 | ETHINYL ESTRADIOL | – | FDA | 2 | 9806355 |
32 | AURKB | SUNITINIB | Inhibitor | FDA | 1 | – |
33 | AURKB | SUNITINIB MALATE | Inhibitor | FDA | 1 | – |