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. 2014 Jul 4;4:5577. doi: 10.1038/srep05577

Table 2. Genetic networks associated with ATRA-induced cell differentiation and drug resistance.

Top 3 ATRA networks Score Focus molecules Molecules in network
Resistance
RNA post-transcriptional modification; DNA replication, recombination, and repair; cell death and survival 55 24 Akt, CD3, CD14, Ck2, CLK2, CLNS1A, CSTF2, CTDP1, cytochrome C, DDX1, EXO1, GTF2H3, histone h3, Holo RNA polymerase II, Hsp70, Hsp90, HSPA4, IFN β, ILF2, NME1, PI4KB, POLR2F, POLR3F, PRMT5, RNA polymerase II, SRPK1, SRSF3, TCEA1, TRA2B, TRAP1, TSTA3, ubiquitin, VDAC2, XRCC5, YWHAQ
DNA replication, recombination, and repair; lipid metabolism; molecular transport 43 20 26s proteasome, caspase, Cg, CRABP2, cyclin A, DUSP3, EIF2S1, EIF3B, ERK1/2, FEN1, GM-CSF, GRK6, Igm, Ikβ, LAMP2, Lh, LIG1, MAP2K1/2, Mek, MMRN1, NFYA, PARP1, PEBP1, PSMB6, PSMC1, PTPRCAP, Rar, Rfc, RFC5, RUNX1, SCARB1, Sos, TCR, TMPO, UNG
Developmental disorder, hereditary disorder, metabolic disease 30 15 ADSL, ARL4D, ATP5G3, CAND2, CNOT3, CNOT10, CNOT11, DENND4A, DFNA5, DRG2, EML4, GBF1, GNPDA1, GNPDA2, MAN1B1, MTRR, MYO1D, PCBD1, PCK2, PGM1, RAVER1, RNF38, RNF114, RNF219, SEC62, SEC63, SPG21, SUPV3L1, TBCE, TMEM230, TNKS1BP1, TRIM52, UBC, UEVLD, ZNF263
Differentiation
Cellular compromise, developmental disorder, hereditary disorder 48 21 Actin, ALB, Ap1, APOC2, CD3, CORT, DTNA, EIF2S1, ERK1/2, F actin, FBN1, FGR, FHL3, growth hormone, insulin, KLK7, KLKB1, laminin, LDL, Lh, MAP2K1/2, Mlc, MSMO1, MYO5A, NID1, NPPA, PAK1, PI3K (complex), POU2F1, PRKG1, RAB27A, SLC12A7, STX6, TGFβ, TXNIP
Small molecule biochemistry, neurological disease, cell death and survival 44 19 Acot1, ACOT8, AMY2B, ARMCX5, ATF5, β-estradiol, CLCA1, CLPTM1, DDIT4, DHCR7, FOS, H1FX, HTT, IL2RB, KCNAB2, MAN1A2, MST1R, NAP1L3, NEDD9, PET112, PLXNB3, REST, SLCO2B1, SPOCK1, ST8SIA5, STEAP1, THRSP, TNF, TP73, TXNIP, UBC, VASH1, VEZF1, ZNF217, ZNF616
Infectious disease, cellular movement, hematological system development and function 17 9 26s proteasome, ACO1, adenosine, Akt, APC, CEACAM6, ERK, F2RL1, FOXF1, GLS, GOT, IFN, IgG, IL-1, IL-12 (complex), IL2RB, IL3RA, interferon alpha, Jnk, KISS1, LTB, MAP3K8, Mapk, MYD88, NADPH oxidase, NF-κB (complex), NLRP3, NOX4, P38 MAPK, Pkc(s), Ras, STC2, TRAP1, uric acid, VEGF