Background
Methods
Materials
NASP overexpression
siRNA transfection
RNA isolation and hybridization of RNA to oligonucleotide arrays
Statistical analysis
Results and discussion
SAM analysis
OVEREXPRESSION | siRNA TREATMENT | ||
---|---|---|---|
Up-regulated | Down-regulated | Up-regulated | Down regulated |
Function/Gene | Function/Gene | Function/Gene | Function/Gene |
Transcription regulators: ATF3, DDIT3, ETV5, FOSL1, IRF7, IRF9, RELB, STAT1 | Transcription regulators: EGR1, FOS, LMO1, NFE2 | Transcription regulators: HMGB2, E2F8 | Transcription/translational regulators: SRF, HOXA10, EIF2C4 |
Transporters: AQP5 | Enzymes: ARL5A, CYP1B1, ME3, GSR, MANEA, GNG2, OGG1 | ||
Enzymes: BIRC3, DDX60, IFIH1, OAS1, OAS3, OASL, PTGS2, RRAD | Others: KR19, PLCXD3 | Ion channel: KCNJ15 | Enzymes: ACADL, ACADSB, GLS, ARL1, CROT, DHTKD1, ENTPD7, FAAH2, GBP3, GATM, LIPH, SEPX1, ZDHHC2, UBE2N, SCCPDH |
Cytokines: CXCL1, CXCL2, CXCL3, TNF, IL11, IL1A, IL6, IL8 | Kinases: PI4K2B, PDGFRB | Kinases: MAP2K1, RFK | |
Growth factors: DKK1, EREG, GDF15 | Transmembrane receptors: TNFRSF11B | Transmembrane receptors: ITGB3, TLR3, ITGA5 | |
Growth factors: FGF2 | |||
Phosphatases: DUSP5, NT5E | G-protein coupled receptors: F2RL1 | Peptidases: CFI, CPA4 | |
G-protein coupled receptors: MRGPRD | Transporters: ATP6V1G3, FMN1, PNMA2, SMC1A, SAA1, SLC25A32 | Transporters: ATP11A, ATP2B4, FABP5, NUPL1, SEC13, SLC25A43 | |
Phosphatases: PPM1K | |||
Others: CLDN1, TNFAIP3, ZC3H12A, HRK, IFI27, IFI6, IFITM1, IGFL2, KRT34, LOC283454, PARP12, PARP9, PHLDA1, PPP1R15A, SAMD9L, STC2, GADD45A | Others: ARL6IP6, C14ORF167, CALB1, CALML4, CGA, CCDC5, CRYAB, FSTL1, FGFBP3, PRR16, SSU72, DTWD2, FST, ZMYM6, HAPLN1, TMSL8, MKX, HCG1815491, KIF5C, SYTL5, MFAP5, PSIP1, LOC100130476, RDM1, MEX3C, PHACTR2, NAP1L5, TMEM64, RASSF8, SLITRK6, ZBED2, MEFF2, TES, RBM17, TMEM80, UBE2E3 | Others: CPEB3, DCBLD2, DCP2, DENND1B, TMEM9B, TNC, ERLIN2, EVI5, GCOM1, HIST1H1C, HIST1H2BK, ZFYVE26, HIST2H2AA3, ZBTB41, NASP, CDCP1, KIAA0329, LOC285535, LONRF1, GPR137B, OSTM1, PCDH7, PPP1R3B, TM9SF4, PPP1R9A, PRRG4, SLAIN2, TUBB3, SHOC2, GLT8D3, CNN1, SPOCD1, DYX1C1, TTC39A, ACTA1, ACTA2, CCDC109A, CCDC126 |
EASE analysis
UP REGULATED | DOWN REGULATED | ||
---|---|---|---|
P-value | GO category | P-value | GO category |
1.56e-011 | immune response | 6.75e-003 | transcription regulator activity |
2.24e-011 | response to biotic stimulus | 2.68e-002 | transcription factor complex |
7.52e-011 | defense response | 3.85e-002 | transcription factor activity |
5.30e-009 | response to external stimulus | 4.21e-002 | DNA binding |
1.16e-008 | cytokine activity | 4.75e-002 | nucleoplasm |
5.89e-008 | receptor binding | ||
7.08e-007 | response to stress | ||
1.12e-006 | response to pest/pathogen/parasite | ||
1.62e-006 | inflammatory response | ||
1.81e-006 | response to wounding | ||
2.39e-006 | innate immune response | ||
8.28e-006 | growth factor activity | ||
9.48e-005 | response to chemical substance | ||
1.96e-004 | regulation of cell proliferation | ||
3.26e-004 | apoptosis | ||
3.31e-004 | regulation of cell cycle | ||
3.36e-004 | programmed cell death | ||
3.46e-004 | chemokine activity | ||
3.46e-004 | chemokine receptor binding | ||
4.59e-004 | cell death | ||
4.87e-004 | death | ||
5.27e-004 | cell proliferation | ||
7.09e-004 | regulation of cellular process | ||
7.72e-004 | regulation of biological process | ||
8.20e-004 | cell cycle arrest | ||
9.52e-004 | regulation of cell proliferation | ||
1.83e-003 | cell-cell signaling | ||
3.38e-003 | response to virus | ||
3.38e-003 | anti-apoptosis | ||
7.00e-003 | cell communication | ||
7.10e-003 | signal transducer activity | ||
9.37e-003 | cell cycle | ||
1.15e-002 | response to abiotic stimulus | ||
1.61e-002 | nucleic acid binding | ||
2.58e-002 | transcription factor activity | ||
3.10e-002 | transcription regulator activity | ||
3.27e-002 | response to DNA damage stimulus | ||
3.27e-002 | regulation of apoptosis | ||
3.31e-002 | response to endogenous stimulus |
UP REGULATED | DOWN REGULATED | ||
---|---|---|---|
P-value | GO category | P-value | GO category |
1.10e-003 | morphogenesis | 1.51e-002 | DNA packaging |
2.10e-003 | organogenesis | 1.59e-002 | cell adhesion receptor activity |
7.68e-003 | chromosome | 1.67e-002 | fatty acid metabolism |
1.00e-002 | nucleic acid binding | 1.73e-002 | muscle development |
1.22e-002 | chromatin | 2.54e-002 | carboxylic acid metabolism |
1.36e-002 | nucleic acid metabolism | 2.95e-002 | nucleosome assembly |
1.69e-002 | development | 3.04e-002 | chromatin architecture |
2.02e-002 | response to radiation | 3.18e-002 | nucleosome |
2.11e-002 | DNA packaging | 3.33e-002 | acyl-CoA dehydrogenase activity |
3.19e-002 | extracellular space | 3.63e-002 | chromosome organization |
4.64e-002 | intracellular transporter activity | 3.90e-002 | nuclear organization and biogenesis |
4.84e-002 | DNA binding | 4.25e-002 | DNA metabolism |
4.96e-002 | transporter activity | 4.39e-002 | chromatin assembly/disassembly |
4.73e-002 | chromatin | ||
4.79e-002 | development | ||
4.87e-002 | chromosome |
IPA analysis
Top bio functions
NASP overexpression
NASP inhibition
Network analysis
NASP overexpression
A. UPREGULATED GENES | ||||
---|---|---|---|---|
Focus genes | Interacting genes | Score | Top functions | |
1 | ATF3, CXCL2, DUSP5, GDF15, IFI6, IFI27, IFIH1, IFITM1, IRF7, IRF9, KRT34, OAS1, OAS3 (includes EG:4940), OASL, PARP9, RELB, STAT1, TNF, TNFAIP3 | Cyclooxygenase, IFN Beta, Ifn gamma, IL1/IL6/TNF, Interferon alpha, Interferon beta, IRF, ISGF3, LDL, MHC Class I, NF-κB, NfkB-RelA, SAA@, Sod, Stat1-Stat2, Tlr | 44 | organismal injury and abnormalities, gene expression, immune response |
2 | CXCL1, CXCL3, DDIT3, DKK1, EREG, OSL1, IL8, L11, IL1A, PHLDA1, PTGS2, PPP1R15A (includes EG:23645) | Akt, ALP, Ap1, Cbp/p300, Creb, ERK, hCG, Hsp27, Hsp90, IKK, IL1, JAK, MAP2K1/2, Nos, P38 MAPK, Pdgf, PDGF BB, PI3K, Pkc(s), PLC, STAT, Tgf beta, Vegf | 25 | cellular growth and proliferation, cellular movement, hematological system function |
3 | BIRC3, ETV5, GADD45A, IL6, RRAD, STC2 | ABLIM, ADCY, CAP2, Ck2, Caspase, Cytochrome C, FSH, DYRK3, Histone h3, Hsp70, IL12, IL1/IL6/TNF, IL1F8, IL1F9, Insulin, Jnk, Mapk, Nfat, NFkB, Pka, Proteasome, Rac, Ras, RNA polymerase II, STAT5a/b, UBR2, Vacuolar H+ ATPase, ZNF274, ZNF675 | 10 | infectious disease, cell cycle, cancer |
B. DOWNREGULATED GENES | ||||
Focus genes | Interacting genes | Score | Top functions | |
1 | AQP5, EGR1, FOS, KRT19, LMO1, NFE2, TNF | ADCYAP1, AKR1B10, ARF4, ASC2, BARX2, BPI, CCL9, COBRA1, CXCL16, DGCR6, EMB, FOXF1, GFPT2, HMBS, IL1/IL6/TNF, IL1F9, JUN, LOC729687, LTBP2, MFHAS1, NFkB, RFTN1, SFI1, SLC7A1, TNIP3, TRAFD1, Vacuolar H+ ATPase, WNT10A | 17 | gene expression, cell cycle, cellular development |
NASP inhibition
Focus genes | Interacting genes | Score | Top functions | |
---|---|---|---|---|
1 | ARL5A, E2F8, GSR, HMGB2, NAP1L5, OGG1, PSIP1, RBM17, RDM1, TMEFF2, TMSL8, UBE2S | APOBEC1, ERBB4, Erbb4 dimer, ERBB4 ligand, ESR2, HCFC1, HINT1 (includes EG:3094), IGH@, KAT5, KPNA2, MAD2L1BP, MAGEH1, NRG3, NRG4, POLE2, RAG1, RCHY1, TBXAS1, TP53, UBE2E3, UBE2V1, WRN (includes EG:7486), WWOX | 25 | DNA replication, recombination, and repair, cellular development, connective tissue disorders |
2 | CALB1, CGA, F2RL1, FST, FSTL1, GNG2, SAA1, SYTL5, TNFRSF11B, ZBED2 | AKR1C14, ARHGAP22, ARHGEF5, ATP9A, C5ORF23, CENPI, ERK, FJX1, FSH, GK7P, hCG, IL2, LOC81691, LOC652955, MARCH3, NFkB, MRPS6, PI4K2A, RAB27A, REGL, STEAP1, Tgf beta, TP53I11, ZFP386, ZNF808 | 20 | reproductive system disease, respiratory disease, immune response |
3 | TES, CRYAB, HAPLN1, KIF5C, MFAP5, PDGFRB, PI4K2B, PNMA2, RASSF8, CCDC5 | AASS, Abl1/2, Cadherin (E, N, P, VE), CAPRIN1, CDKN2A, CNN2, CTNNB1, DLL3, FRMD6, GLRX2, hydrogen peroxide, KIFC1, KLC3, KRT1, LSR, MLXIP, NOTCH1, PMEPA1, PXN, SRC, SRFBP1, TAX1BP3, TGFB1, TOB2, YWHAG | 20 | cancer, cell death, cell cycle |
Focus genes | Interacting genes | Score | Top functions | |
---|---|---|---|---|
1 | ACTA1, ACTA2 (includes EG:59), ARL1, ATP2B4, CNN1, DCBLD2, FGF2, HOXA10, ITGA5, ITGB3, MAP2K1, SEC13, SHOC2, SRF, TNC | Actin, Akt, Alpha actin, ERK, ERK1/2, FSH, IKK, Integrin, Jnk, Mapk, Mek, Pdgf, PDGF BB, PI3K, Pkc(s), PLC gamma, Pld, Ras, Tgf beta, Vegf | 31 | cellular assembly and organization, cell-to-cell signaling and interaction, viral infection |
2 | CDCP1, CROT, DYX1C1, ERLIN2, GCOM1, GLS, GPR137B, HIST2H2AA3, PPM1K, SLAIN2, SPOCD1, TTC39A, TUBB3, ZDHHC2 | beta-estradiol, F2, HSPA1A, HSPA1L, IFRD2, KYNU, MAPK11 PREDICTED, VCP, MFHAS1, MMD, NFRKB, NOS3, PGLYRP1, SAMD4A, SLC16A5, SPR, TNF, TXN2, YWHAZ, ZDHHC8, ZNF267 | 28 | cardiovascular system development and function, tissue morphology, organismal development |
3 | ACADL, ACADSB, CPEB3, ENTPD7, EVI5, CFI, CPA4, TLR3 GATM, LIPH GBP3, RFK, PPP1R9A, OSTM1 | 9330129D05RIK, ACAD8, ACAD9, ACAD10, ACAD11, Acyl-CoA dehydrogenase, C3, CDKN2A, CFHR3, CFHR5, F Actin, Glycogen synthase, GTP, heparin, IL4, IWS1, NFkB, NFYB, Pka, PLK1, RAB1A | 28 | lipid metabolism, molecular transport, small molecule biochemistry |
4 | DCP2, FABP5, GLT8D3, HIST1H1C, HIST1H2BK, NASP, NUPL1, PCDH7, PPP1R3B, SEPX1, TM9SF4, UBE2N | ANXA9, DHX8, ERLIN1, FASTKD2, HNF4A, IL1B, MGEA5, MRTO4, NAT13, NUDT11, NUP62, OTUD7B, PHPT1, PSMC3, REXO2, SEC11A, MEM176B, TMEM189-UBE2V1, TRAF6, TRAFD1, Ube2n-Ube2v1, UHRF1, WRNIP1 | 23 | cell signaling, cancer, cellular compromise |