Integrated Analysis of a Gene Correlation Network Identifies Critical Regulation of Fibrosis by lncRNAs and TFs in Idiopathic Pulmonary Fibrosis

Table 1

DEGs were identified from three datasets, including 262 upregulated and 191 downregulated genes in IPF compared with normal lung tissues (upregulated genes were defined with as the cutoff criterion. The opposite was defined as downregulated genes).

DEGs	Gene names
Upregulated	SULF1, DEAF1, SCG5, DSG2, SLC1A4, CCND2, KCNN4, ST6GAL1, SLC38A1, SEC11C, XPOT, DPY30, PFKP, DDB1, HEPH, CXCL13, ATXN10, SEL1L3, CIAO1, CCL19, STARD5, SLFN12, ROR2, VAT1L, FPGT, GMPPA, COL18A1, COL7A1, PIGF, LMO4, FAM120A, SLC29A3, TCFL5, IGFBP2, UQCRQ, CCNA2, TWSG1, TCTN3, ASPN, PAM, BPIFB1, FAIM, FBLN2, SCARA3, COMP, ABCC5, DIO2, CHEK2, MCM4, TM9SF2, NAB1, DGKA, PTGFRN, FAT1, DOK5, CNIH1, ACTN1, PLA2G12A, MAGED1, ALG1, TWIST1, TRIM5, RCN2, CXCL14, ARMC1, STMN3, HMCN1, WDR5B, CROT, LEF1, TMEM14A, PLA2G4A, FKBP10, ABCC3, SPR, ROBO1, OXR1, CRLF1, TRIAP1, KDELR3, DIRAS3, BBS2, TGFB3, LGMN, CDK2AP1, CXCL12, RRM2, STRBP, TSPAN6, DAP, COL6A3, FZD6, TDO2, GMDS, PPP2R5E, SUPT7L, ZKSCAN7, CDKN3, CNTNAP1, IGF1, GSS, LRRC8D, TMEM98, TRIM2, LTBP1, BACE2, BRD8, COLEC11, FXN, PAFAH1B3, PGAM1, COL5A2, AOC1, ANTXR1, TMEM69, IMPACT, NET1, MXRA5, RCN1, MYO1E, DUSP23, CDH3, RHOD, CYP2S1, POSTN, ICMT, PDLIM4, C1QTNF6, ACVR1, SYTL2, PLA2G7, MFAP2, ZDHHC13, TMED10, ALDH1A3, SLN, CPOX, CDKN2C, PPIC, XRCC5, CLDN1, NSG1, ITGA7, R3HDM1, ERGIC2, TRIM36, EYA2, RPL39L, CCL13, RBP5, DONSON, SERPINB5, TXNDC15, HOMER3, ARL1, UBE2E3, CRYM, MEOX1, TMEM45A, COL15A1, ATP1B1, LDLRAD4, STEAP3, NABP2, BDKRB2, DCLK1, CFH, TRO, ECM1, PFN2, IL13RA2, MYOF, FHL2, CADPS, ITGAV, PCNA, PTK7, KIF2C, MEGF8, BMP4, PDCD2L, PRMT6, TP53BP1, OSBPL6, FMO1, PDE1A, PBX3, ELOVL4, ATF7IP, SYNDIG1, TMEM158, CFI, ALDH3A1, CKAP2, MRPL2, COL14A1, EGFL6, LHX6, THBS2, RRM1, YLPM1, TM7SF3, MLEC, CFB, BCL11A, GPR87, ZNF436, CLNS1A, ATIC, LGR4, CYP24A1, SEMA3C, PDGFC, TP63, ARMCX2, NUSAP1, ASB2, SLC39A6
Downregulated	MKLN1, ECHDC3, RAB32, SLC25A51, HOPX, MATN3, MAP2, ARHGAP6, EPB41L5, NRGN, HEY1, PCTP, ACVRL1, TBX5, ERMP1, NAGA, MPP1, TXNIP, LRRN3, FLOT1AATK, RCL1, CSF3R, ANXA3, TEK, GRK5, HES1, HSPA1L, GATA6, EMP2, SLCO2A1, PMM1, STARD13, SEC14L1, SPTBN1, GHRL, TSPAN7, NEBL, ZNF655, TMEM11, UIMC1, NCOA3, ZFP36, CREBBP, LDLR, RAB20, SERTAD1, PPFIBP1, REPS2, ELF1, CALCOCO2, CSRNP1, GPM6A, DLL4, FPR1, CARHSP1, ADARB1, LMO7, RCOR1, LRRC32, CTNNBIP1, CA4, PADI4, OSGIN1, CXCL2, EGFR, CHI3L2, LPIN2, ANKHD1, ARHGEF4, ARHGAP29, VAMP5, RAI2, CYTIP, PRX, IER5, DNM2, IL17RA, BHLHE40, SLC39A8, RAPGEF5, PTPRM, CNOT8, DLC1, TLK2, EPAS1, PRELP, MAFF, ABTB1, HSD17B6, NDEL1, HYAL1, HECA, HSPB8, DNAJB1, CDH13, RGS16, PTPN12, CD55, TIPARP, CRYAB, CD36, NUP153, PTPRB, ITSN2, TNNC1, MAPT, THBD, CDKN2D, AOC3, P2RY1, ZBTB16, CSF3, EDNRB, FAM167A, SRGAP2, SLCO1A2, DAPK2, AGTR1, RIMKLB, ASRGL1, ANG, CCK, BCL2L13, OSGIN2, ACSM5, KIAA0040, KDR, FUT1, DOCK9, GADD45G, CLDN5, LIFR, STXBP6, GPR4, S1PR1, SLC1A1, PLAG1, EDA, DENND3, IDI1, KHDRBS3, CLEC1A, INMT, MPP3, PLLP, MTSS1, FSTL3, CRTAC1, GTF2IRD1, F3, KLF10, KLRD1, FBLN5IZUMO4, PIR, MAOA, C1QL1, THRB, RNF182, ALDH6A1, FAM49A, ST6GALNAC3, SSFA2, SLC25A24, AMPH, ADAMTS8, PLSCR1, BCKDHA, STXBP4, FLRT3, AOX1, SYAP1, RLF, SSH2, DERA, PIM1, STARD3NL, SUN2, SEPP1, IL1R2, EIF2A, FAH, METTL7A, EIF4E3, CHRM2, 1-Mar, PDK1, TJP2, RASL11A, NKX3-1