1
Table SIII IPA network analysis of the significantly deviated and over twofold
upregulated (A) or downregulated (B) genes in PC-3/FGF-8b cell vs. PC-3/mock
cells.
A. Network
ID
1
Genes in Network
Score
ADCYAP1, CALD1, CD44, CDH5, CKLFSF3,
COL18A1, CTNNB1, E2F1, EFNB2, EGFR, FBLN2,
FGF3, FGF8, FGF10, FGFR1, FGFR3, FGFR4,
IFITM1, MAGEF1, MAPK1, MDK, MSX1, RGS12,
SDCCAG33, SHC1, SPARC, SPRY2, SRC, SRF,
TNF, TNFRSF21, TNXB, TRIP6, VEGFB, WNT1
AK1, ATAD2, BTG2, CABLES1, CCNG1, CDKN2A,
CITED4, CRIP1, CTCF, DDR1, DHFR, E4F1, EP300,
FEN1, GTSE1, HMGB2, HNF4A, MDM4, PLAGL1,
POLD3, RRM1, RRM2, RRM2B, TBX3, TFAP2A,
TFAP2C, TM7SF2, TOP1, TP53, TP53INP1, TWIST1,
VRK1, WIG1, WNT1, WRN
24
No. focus
genes
12
8
5
B. Network
ID
1
Genes in Network
Score
ALDH1A3, ATXN3, CCRK, CDK2, CXCL1, CYBA,
ELL2, FNBP1, FST, G1P2, LAMA2, LAMA3,
LAMB3, LAMC2, MMD, NEDD8, PC4, PIGR,
PSMA1, PSMA2, PSMA3, PSMA4, PSMA6, PSMB1,
PSMB2, PSMB6, PSMB8, PSMB10, SIM1, SKP1A,
TFPI2, TNF, UCHL3, VDR, ZNF365
22
No. focus
genes
15
2
ACTB, ANXA2, CALB1, CTNNB1, CYTB, DDIT3,
DDX17, EDIL3, FBXO2, GDF15, GH1, HNRPH1,
HSPD1, ID1, ID3, IFI16, LDHA, LDHB, LGALS3,
MMP7, MYC, MYCBP, PNN, POLR2A, PRDX3,
RPL7, RPL22, RPS23, SUMO1, TCF4, TFAP2A,
TRRAP, UQCRH, XDH, ZRF1
ACP5, BARD1, CALM2, CITED2, CKS2, CTSK,
DCN, DUSP1, EPRS, ERBB2, GDF15, HSPB2, IARS,
ID1, IL17F, IL6, JDP2, KLF4, KLKB1, LYZ, MIG-6,
P4HA1, P4HA2, PCAF, RPL11, RUNX3, RXRB,
SLPI, SMURF2, SPHK1, STATIP1, SURB7,
TADA3L, TGFB1, TP53
ACTB, CALM2, CCT3, CCT4, CCT5, CCT7, CCT8,
CCT6A, CKB, CRYAB, CYCS, E2F1, EXOSC10,
FDX1, FOS, HAT1, HCRT, HIST2H2AA,
HIST2H2BE, HSPB1, HSPD1, HSPE1, IL15, IPO9,
JRK, KNTC2, PMAIP1, PRF1, PSAP, RBP1, RPL26,
RPS7, RPS24, TXNRD1, ZFP36
22
15
20
14
Cancer, cell cycle,
reproductive
system
20
14
AXL, BCL2L1, BCL2L10, BIK, C1QBP, CBL,
CCL26, CLEC11A, CYBB, E2IG5, ETF1, F12, GAB1,
GAS6, HINT1, HRK, IGFBP3, IL13, IL18, KIT,
KITLG, MAPK1, MCL1, MUC1, NCF2, NMU,
OPRM1, OXT, OXTR, PRKCQ, PRKD1, RASD1,
RPS3A, SLC43A3, STAT6
BAX, BMP4, BRCA1, CCND1, DDIT3, EGFR, EGR1,
ERBB3, ERBB4, ESR1, ESR2, GNRH1, GRB2,
ICAM1, IGF1, IGF1R, IGFBP3, IL8, INSR, ITGA5,
KNG1, LEPR, MAP3K1, NPPA, PDGFRB, PRKCD,
PTH, SLPI, SNX1, SNX2, SNX6, TFF1, TGFA,
WNT1, WT1
16
12
2
3
Energy
production,
nucleic acid
metabolism, small
molecule
biochemistry
Cell death,
cellular
development,
cellular growth
and proliferation
Cellular growth
and proliferation,
cell death, cellular
development
2
3
4
5
6
Top Categories
Embryonal
development,
cellular growth
and proliferation,
cellular movement
Gene expression,
cancer, DNA
replication,
recombination and
repair
Top Categories
Dermatological
diseases and
conditions,
genetic disorder,
cell-to-cell
signaling and
interaction
Cell death,
connective tissue
gene expression
2
Table SIII footnote: Top networks and their top three network function categories
generated by IPA for differentially (over twofold changed) expressed genes in FGF-8transfected PC-3 cells. The score is the negative log of p and indicates the likelihood
of the focus genes in a network being found together as a result of chance. Therefore,
scores of 2 have at least 99% confidence of not being generated by chance alone. No.
focus genes refers to the genes affected by FGF-8 transfection within a network. Bold:
genes affected by FGF-8; standard text: genes in network not affected by FGF-8.