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Table 3 The investigated pathways verified by IPA

From: Differential responses in placenta and fetal thymus at 12 days post infection elucidate mechanisms of viral level and fetal compromise following PRRSV2 infection

Pathway

Gene namesa

Number of genes on NanoString assigned to pathway manuallyb

Number of genes on NanoString assigned to pathway by IPAc

Total number of genes in IPA pathwayd

Coverage of IPA pathway (%)e

Acute Phase Response Signaling

C2, C3, C4A, C4BPB, C5, CFB, FN1, FOS, IKBKB, IKBKE, IL1A, IL1RAP, IL33, IL6R, JAK2, KRAS, MAP2K4, MAP3K7, MAPK14, MAPK8, MYD88, NFKB1, NFKB2, NFKBIA, NFKBIE, OSM, PIK3CG, RIPK1, RRAS, SAA4, SERPING1, SOCS3, SOCS6, SOD2, STAT3, TAB1, TNF, TRAF2, TRAF6

0

39

181

22%

Antigen Presentation Pathway

B2M, CTSS, IFNG, MHCI related, PSMB8, PSMB9, SIGLEC1, SLAMF6, TAP1, TAP2

4

6

39

15%

Apoptosis Signaling

BAK1, BCL2A1, BCL2L1, BID, BIRC3, BIRC6, BNIP3, CASP10, CASP3, CASP8, CASP9, CDK1, FAS, FASLG, GZMB, IKBKB, IKBKE, KRAS, MAP2K4, MAPK8, MCL1, MYC, NFKB1, NFKB2, NFKBIA, NFKBIE, PARP1, PLCG1, PRKCQ, RRAS, TNF, TOPOII, TP53

4

29

99

29%

B Cell Development

CD19, CD40, CD79A, CD79B, CD86, DNTT, IL7R, PTPRC, SPN

0

9

36

25%

B Cell Receptor Signaling

BCL2A1, BCL2L1, BLNK, CD19, CD79A, CD79B, ETS1, FCGR2B, GSK3B, IKBKB, IKBKE, KRAS, LYN, MAP2K4, MAP3K7, MAPK14, MAPK8, NFKB1, NFKB2, NFKBIA, NFKBIE, PIK3AP1, PIK3C2B, PIK3CG, PRKCQ, PTK2B, PTPRC, RRAS, TNFRSF13B

1

28

190

15%

Complement System

C1QA, C2, C3, C3AR1, C4A, C4BPB, C5, C5AR1, CD55, CFB, CR1, ITGAM, ITGB2, MASP1, SERPING1

0

15

38

39%

HIF1-alpha Signaling

ARNT, EGLN1, EGLN2, HIF1A, HIF1AN, HIF3A, KRAS, MAPK14, MAPK8, NOS3, PGF, PIK3C2B, PIK3CG, RRAS, TP53, VEGFA, VEGFB, VHL

2

16

115

14%

HMGB1 Signaling

CCL2, CXCL8, FASLG, FOS, HMGB1, ICAM1, IFNG, IFNGR1, IL12A, IL12B, IL1A, IL33, KRAS, MAP2K4, MAPK14, MAPK8, NFKB1, NFKB2, OSM, PIK3C2B, PIK3CG, RHOC, RHOH, RHOU, RND2, RRAS, TLR4, TNF, TNFSF10, VCAM1

0

30

165

18%

IL-10 Signaling

ARG2, CCR5, CD14, FCGR2B, FOS, IKBKB, IKBKE, IL10, IL1A, IL1RAP, IL33, MAP2K4, MAP3K7, MAPK14, MAPK8, MIF, NFKB1, NFKB2, NFKBIA, NFKBIE, SOCS3, STAT3, TAB1, TNF, TRAF6, TYK2

1

25

73

34%

iNOS Signaling

CD14, FOS, HMGA1, IFNG, IFNGR1, IKBKB, IKBKE, IRAK2, IRF1, JAK2, JAK3, LY96, MAPK14, MYD88, NFKB1, NFKB2, NFKBIA, NFKBIE, STAT1, TAB1, TLR4, TRAF6, TYK2

0

23

48

48%

Interferon Signaling

BAK1, FCGR1A, IFIH1, IFIT1, IFIT2, IFIT3, IFITM1, IFNA1/IFNA13, IFNB1, IFND1/IFND2, IFND3/IFND4/IFND10, IFND5/IFND6/IFND9/IFND11, IFND7, IFND8, IFNE, IFNG, IFNGR1, IFNW2, IFNW4/W5, IRF1, ISG15, ISG20, JAK2, MX1, OAS1, PSMB8, STAT1, STAT2, TAP1, TYK2

12

18

36

50%

NFKB Signaling

CASP8, CD40, FCER1G, GSK3B, IKBKB, IL1A, IL33, KRAS, LCK, MAP3K7, MAPK8, MYD88, NFKB1, NFKB2, NFKBIA, NFKBIE, PIK3C2B, PIK3CG, PRKCQ, PRKCZ, RIPK1, RRAS, TAB1, TAB2, TLR10, TLR2, TLR4, TLR7, TLR8, TLR9, TNF, TNFAIP3, TRAF2, TRAF6, ZAP70

0

35

179

20%

Production of Nitric Oxide and Reactive Oxygen Species in Macrophages

ARG2, FOS, GP91-PHOX, IFNG, IFNGR1, IKBKB, IKBKE, IRF1, IRF8, JAK2, JAK3, LYZ, MAP2K4, MAP3K7, MAPK14, MAPK8, MPO, NCF1, NCF2, NCF4, NCR1, NCR2, NFKB1, NFKB2, NFKBIA, NFKBIE, PIK3C2B, PIK3CG, PLCG1, PPM1J, PPP1R14C, PPP2R1B, PRKCQ, PRKCZ, PRKD1, RHOC, RHOH, RHOU, RND2, S100A8, SAA4, SEPX1, STAT1, TLR2, TLR4, TNF, TYK2

4

43

194

22%

Protein Ubiquitination Pathway

B2M, BIRC3, BIRC6, IFNG, PSMB8, PSMB9, PSMD8, PSME2, TAP1, TAP2, TRAF6, USP18, VHL

0

13

277

5%

Senescence Pathway

ATM, AXL, CCNB1, CDC25B, CDK1, CXCL8, ETS1, IFNA1/IFNA13, IFNB1, IFNK, IFNW1, IKBKB, IKBKE, IL1A, ITPR3, KIF23, KRAS, MAP2K4, MAP3K7, MAPK14, MCM2, MCM3, MYC, NFKB1, NFKB2, PARP1, PCNA, PIK3C2B, PIK3CG, PKMYT1, PLK4, PPM1J, PPP2R1B, PRKCZ, PTTG1, RRAS, SAA4, SOD2, TLR2, TP53, TRAF6, VHL, WEE1

10

33

280

12%

T Cell Receptor Signaling

CD244, CD3D, CD3E, CD3G, CD4, CD48, CD8A, CD8B, FOS, GRAP2, IKBKB, IKBKE, ITK, KRAS, LAT, LCK, LCP2, LY9, MAP2K4, MAPK8, NFKB1, NFKB2, NFKBIA, PIK3C2B, PIK3CG, PLCG1, PRKCQ, PTPRC, RRAS, TEC, ZAP70

3

28

110

25%

Th1 and Th2 Activation Pathway

CCL4, CCL8, CCR5, CD3D, CD3E, CD3G, CD4, CD40, CD86, CD8A, CLEC4G, ICAM1, ICAM3, IFNA1/IFNA13, IFNG, IFNGR1, IL10, IL12A, IL12B, IL1B1, IL33, IL6R, IRF1, ITGB2, JAK2, JAK3, KLRD1, LTA4H, LTC4S, NFKB1, PIK3C2B, PIK3CG, PRKCQ, SOCS3, STAT1, STAT3, STAT5A, TYK2

7

31

172

18%

Tight Junction Signaling

ACTG2, CLDN1, CLDN3, CLDN4, CLDN7, FOS, HS3ST3B1, MYL4, MYL7, NFKB1, NFKB2, PPM1J, PPP2R1B, PRKCZ, TJP2, TJP3, TNF

1

16

168

10%

Toll-like Receptor Signaling

CD14, FOS, IKBKB, IL12A, IL12B, IL1A, IL33, IRAK2, IRF5, LY96, MAP2K4, MAP3K7, MAPK14, MAPK8, MYD88, NFKB1, NFKB2, NFKBIA, TAB1, TAB2, TLR10, TLR2, TLR4, TLR7, TLR8, TLR9, TNF, TNFAIP3, TRAF6

1

28

77

36%

TR/RXR Activation

DIO1, DIO2, DIO3, HIF1A, PIK3C2B, PIK3CG, SLC16A10, SLC16A2, SLCO1C1, TG, THRa, THRb

5

7

91

8%

TREM1 Signaling

CASP1, CCL2, CD40, CD83, CD86, CXCL8, FCGR2B, ICAM1, IL10, ITGA5, JAK2, LAT2, MPO, MYD88, NFKB1, NFKB2, NLRP3, NOD1, PLCG1, STAT3, STAT5A, TLR10, TLR2, TLR4, TLR7, TLR8, TLR9, TNF, TREM1, TYROBP

0

30

76

39%

Otherf

ADAM17, ALOX5, ALOX5AP, AZU1, CDH16, CLEC12A, CLEC7A, CTSB, CTSC, CTSV, CXCL10, CXCR2, DEFB1, DHX58, GBP5, HO2, IGSF6, ITGB7, MBL1, MDGA2, NLRX1, NPPA, P4HA1, PAK1, PECAM1, PID1, PTGS1, PTGS2, RELT, S100B, ST14, STAB1, TBP10, TTC7A, YWHAZ

35

0

N/A

N/A

House Keepingg

HMBS, HPRT1, IPO8, MAU2, RPL32, RPL4, SDHA, STX5, GAPDH, TOP2B

10

0

N/A

N/A

  1. aThe gene names of those tested on the NanoString that were assigned to a given pathway by Ingenuity Pathway Analysis (IPA) software (accessed on February 27, 2020) with genes in bold manually assigned to the pathway based on relevant functional annotation from IPA
  2. bThe number of genes tested on the NanoString that were manually assigned to a pathway based on relevant functional annotation from IPA
  3. cThe number of genes tested on the NanoString that were assigned to a pathway by IPA software
  4. dThe total number of genes in the IPA database assigned to a given pathway
  5. eThe percent coverage of a given pathway calculated by dividing the columns (c/d)*100%
  6. fGenes tested on the NanoString that were not assigned (automatically by IPA or manually) to any of the investigated pathways
  7. gThe genes tested on the NanoString used for normalization of the count data
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BMC Genomics

ISSN: 1471-2164

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