Table 3 The downstream effects of the upstream regulators from the comparison of Vm vs. Vp.

From: Combating viral contaminants in CHO cells by engineering innate immunity

Virus

Consis-tency score

Total nodes (TF, TG, BP)*a

Transcription factors (TF) *b

Target genes (TG)*c

Biological Process (BP)*d

Relations*e

VSV

8.00

22

(4, 15, 3)

STAT1, IRF3, IRF5, IRF7

CXCL10, DDX58, EIF2AK2, IFIH1, IL15, ISG15, JUN, Mx1/Mx2, OASL2, PSMB10, PSMB8, PSMB9, SOCS1, TAP1, TNFSF10

Inhibit

Replication of virus; Quantity of lesion.

Activate

Quantity of CD8+ T lymphocyte.

2/12 (17%)

EMCV

12.16

29

(6, 19, 4)

STAT1, IRF3, IRF5, IRF7, TRIM24, ATF4

BST2, CXCL10, DDX58, EIF2AK2, EIF4EBP1, IFIH1, IL15, ISG15, Mx1/Mx2, OASL2, PSMB10, PSMB8, PSMB9, SLC1A5, SLC3A2, SLC6A9, SLC7A5, TAP1, TNFSF10

Inhibit

Replication of virus; Transport of amino acids.

Activate

Quantity of CD8+ T lymphocyte; Quantity of MHC Class I on cell surface.

3/24 (13%)

EMCV

7.91

18

(2, 10, 6)

CCND1, SMAD4

AREG, CCND2, EREG, GJA1, HSPA8, ITGAV, NFKBIA, PTGS2, SOX4, SPP1

Inhibit

Arthritis; Cell cycle progression; Cell viability; Growth of ovarian follicle; Proliferation of cells.

Activate

Edema.

7/12 (58%)

EMCV

6.96

19

(2, 10, 7)

MKL1, VDR

CAMP, CCL2, HLA-A, ICAM1, IL6, MMP9, PTGS2, RELB, SPP1, TNC

Inhibit

Cancer; Quantity of interleukin; Rheumatic Disease; Development of body trunk.

Activate

Cell death of connective tissue cells; Nephritis; Organismal death.

7/14 (50%)

Reo-3

5.61

21

(4, 14, 3)

GFI1, NR1H3, NRIP1, PPARG

ACACB, CAV1, CD36, CSF3, ETS1, ID2, IL6, LDLR, LPL, NFKBIA, PDK2, PDK4, PPARA, SLC2A1

Inhibit

Oxidation of carbohydrate; Production of leukocytes; Quantity of vldl triglyceride in blood.

1/12 (8%)

  1. *aConsistency score is to measure the consistency of a predicted network by IPA with the literature evidences.
  2. *b,cThe upstream regulators (STAT1 is highlighted in bold face) and the antiviral relating genes.
  3. *dThe biological functions known to associated with the regulatory networks annotated by the IPA.
  4. *eThe number of identified relationships and the total relationships that represent the known regulatory relationships between regulators and functions supported by literatures annotated by the IPA.
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