PPI Analysis in String Database

Question

[anasjamshed]

I put my 502 DEGS in string database to analyze PPI and 474 appears in my network now I want to select DEGS with the threshold score (median confidence) >0.4 but unable to do this

REG1A
FSTL3
AFAP1L2
HCST
TNMD
IFNLR1
SERINC5
TRIL
ATP6V0A4
TSPYL5
C1QB
LOC642441
PRDM16
TSPYL1
NKAIN4
NTHL1
ARHGAP18
S100A9
GPX4
OBSCN
IGFLR1
ISG20
PSMB9
PRRC1
BST2
NKAP
FCGR1B
C2
RAB14
NCAPH2
STX4
ARNT
PTPN2
S100B
LIMCH1
ZC3HAV1L
BCL9
TYROBP
LRPPRC
NCF4
STAT1
EFHD2
CADM4
FLAD1
C9orf16
ODF3B
MBOAT2
NR2F2
BCOR
MEX3D
U2SURP
RAB11FIP1
GZMH
LSM7
PLEKHO1
TSTA3
EIF3G
TCF7L2
CLDN8
SCO2
TPRN
PLEKHM3
GMCL1
NUDT1
NHSL1
GBP2
PSMB10
ASAP2
ATP9B
TFAP2A
C1QC
IRS2
LOC105373341
KDM6A
ZNF576
CDKN3
UACA
RAD51D
WDR20
PCDHB16
ZNF236
ADGRF5
NOSIP
HIPK2
GLTP
ASXL3
LRG1
CORO1A
TAP1
MECP2
RPS19BP1
CDH1
RSRP1
MCM3AP-AS1
ZNF677
CADM1
RPS15
RPS8
NDUFA3
GART
GIGYF2
TARSL2
HOOK3
LIFR
ASXL2
ATP7B
RBM25
B4GALT7
PLCL1
PCDHB3
MAPK1IP1L
UBXN7
TMEM54
PYCARD
ZBTB41
PPP1R14B
DDIT3
PIN1
TRPC1
PTTG1
CD79B
HNRNPA0
NDUFA11
FRY
EVI5
EMP3
FRMD3
AIP
ELMSAN1
AOAH
LOC101928419
MED13
ELF5
PER2
FBXL17
CARD16
FAAP20
ATP5J2
CASZ1
PROCR
PNPLA4
RIT1
TFPT
SDF2L1
C5orf22
PHPT1
CNTN1
CAMSAP2
APBB2
DACT1
TIMM13
SAC3D1
PRKAA1
CXCL13
CCDC109B
PM20D2
MRPL30
DLAT
RNPC3
1-Sep
DIRC2
THSD4
C4orf48
NRSN2-AS1
MIR155HG
CNPY3
APOBEC3F
MRPL54
CFB
SMIM1
OGFOD3
EEF1D
MINOS1P1
DNLZ
ACAP1
C3
C6orf62
FGF9
KMT2D
PPA2
BAD
TAOK1
PSMB8-AS1
GBP5
CLCN3
FRMD4A
PHTF1
PDE12
TRAPPC5
NCF1
NDUFS6
TFCP2L1
NAP1L2
PLA2G7
MTMR4
NLRC5
SLC35G1
SMARCA2
NUCKS1
LIPH
NNMT
9-Mar
BTN3A2
RAPH1
YTHDC2
ADTRP
CCDC167
NEDD4L
GATAD2B
BMPR1B
PMS2P4
SAMHD1
LMLN
RIMKLB
PPM1K
ESRRG
PPP1R7
ELOVL5
MPPED2
BAX
SLAMF8
HCG4
STK19
ZADH2
MSI2
ZNF101
PRR15
PCNXL2
LOC645166
TCEANC
CD14
RARRES3
STARD10
AASS
SLC16A7
SEPP1
POLR2I
RNF144A
CPNE3
CXCR6
FAM63B
HMG20B
CST6
PAPD4
LTB
IL32
FOLR2
MCM9
TRAK1
SYCE1L
ZNF264
SGK2
SCARB2
SLC12A2
HCP5
SRSF11
SCAMP1
THSD7A
ZNF836
KCNJ3
COBLL1
SPIN4
NEK6
PTPN13
ABCA5
SETBP1
DUS1L
APPL1
ADGRF1
CENPU
MAP4K4
VTI1A
GMEB1
SMURF2
CXCL10
GZMK
RRM2
SLA
IGSF6
ZNF683
IFI35
GABRA2
PTRH1
CCL13
7-Mar
LTF
BIRC5
PGLS
LINC00491
GVINP1
INHBA
PLAGL1
PIK3C2B
WSB1
GRHL2
MED4
BID
E4F1
NIPAL3
SPRED2
KDM5C
LYZ
WNT6
DNMBP
ZNF709
C11orf71
AKT3
RP2
S100A1
CNOT7
EIF4E
PIGW
VPS51
WAC
TAF15
C1QA
N4BP2L2
BIN2
CNNM3
CRIPT
IFITM1
EDEM3
GYPC
PLAC8
ICAM3
SLC26A7
XCL1
PTBP3
CLEC2B
HCK
SNX20
IRF7
AIF1
SELM
RNASEH2C
CFD
POU6F1
ADA
S100A8
C11orf80
RORB
TBC1D4
IDO1
6-Mar
PDLIM4
CCDC22
THNSL1
SMAD4
CD3D
KIAA0101
CHPF2
CCL5
FKBP11
ABCG1
CCL19
AIM2
LOC284578
COL4A3
ATP6V0D2
CXCL11
CST7
LOXL1-AS1
APOC1
TRDV3
REPS2
STAT4
DENND4C
NFIB
MXRA5
GZMA
DNPH1
CPE
LSP1
CSTA
ZKSCAN8
MGMT
NKG7
SEMA6D
C9orf9
FCGR1A
AGR2
SART1
NCF2
LOC100272216
CFAP97
XK
SLC6A8
RPL22L1
PDE4A
TXNIP
MFSD6
GPR171
ERMP1
TP53INP2
TRA2A
THBS1
MS4A4A
LACTB2
FECH
OGT
CD52
LGR5
RPH3AL
EFNA5
SIM1
DAPL1
DCTN2
MMP7
ALKBH5
STAB1
LARP7
ENAM
ACKR4
NOTCH3
TIMP1
SERTAD4
FARP1
LINC00954
LAPTM5
KRT222
DICER1
KIF16B
DACH2
MAGI1
ADAMTS5
PTPRN2
FAM26F
OGG1
DNAL1
PLEK
ARHGAP9
HMGCS2
MAP4K1
LST1
CRK
TM2D1
PPDPF
GZMB
CRLS1
PNKP
ASL
SLA2
MDM4
LRRC2
LAIR2
ATXN7
SLC1A3
C1orf162
SLC5A3
CLNK
EGF
TNFAIP8L2
AGXT
PRKAR1A
APOBEC3G
PRSS16
LOC389332
CASP1
TRDC
SLC25A37
AQP6
GNE
GSE1
IGHM
CXCL9
ABHD12
CTTNBP2
CCL18
MAGEB4
LRRC43
CD48
CLSTN2
ZFAND6
CMTM4
PPP2R1B
LCP2
CALM1
SIGLEC1
VSIG4
CDKN1A
C1S
SPATA33
ITGB2-AS1
CD163
NAA25
LIN37
MIRLET7DHG
NPTN-IT1
RPS4Y1
MTPN
DDX17
ACTA2
GBP1
ITGAL
FAM84A
MAP3K15
SLAMF7
PRKCDBP
PTPRC
CFLAR
METTL7A
BCL2A1

Can anyone help me plz?

[Ram]

It looks like you copy-pasted the gene list in Excel at some point. It's not safe to do that - read this paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7

For example, your gene list has the Excel artifacts 1-Sep and 9-Mar, which are Excel's way of "reading" genes probably named SEPT1 and MARCH9

[anasjamshed]

i dont copy paste it comes from tobtable functions in R

[Ram]

All I can say is, it has been through Excel at some point. 1-Sep is not a gene symbol, it's Excel's interpretatioon of SEPT1, which is a gene symbol.

[WouterDeCoster]

Which used to be a gene symbol, but is now renamed to SEPTIN1 (see this article)

Answer 1

[scooter]

If you want to change the confidence limits of the STRING network, there are a couple ways to do that. First, you can switch the confidence limit by using the menu Apps->STRING->Change confidence. This will remove edges that don't meet your new confidence cutoff. A better way to explore the networks is to use the STRING Results Panel. Click on the Edges tab in the results panel and you will see a "Score" slider in the top. You can adjust that slides and it will hide edges that don't meet you cutoff.

-- scooter

[anasjamshed]

how brother I don't understand the procedure?