Table 4 Genes upregulated by IL3IgG- versus IL5IgG-activated eosinophil conditioned medium and versus control media (medium only and rhIL3IgG) in fibroblasts

BMP8B (secreted)

Bind TGF-ß receptors– Activates SMAD

Network 1: inflammatory response (Additional file 2: Figure E1)

C3 (secreted)

Modulates inflammation – Antimicrobial activity

Target molecule (Table 2); Regulated by TNF, IL1B, IL6, NFkB, MYD88, RELA, STAT1 (Table 3); Networks: immune response, remodeling and lipid metabolism (Figs. 2, 3, 4); Network 2: cell trafficking (Additional file 8: Figure E2)

C8A (secreted)

Antimicrobial activity

CH25H

Cholesterol-Lipid metabolism

Target molecule (Table 2); Regulated by TNF, OSM, STAT1 (Table 3); Networks: immune response, lipid metabolism (Figs. 2 and 4)

CHADL (secreted)

Inhibits collagen fibrillogenesis

CIDEC

Insulin sensitivity

Regulated by TNF (Table 3); Network 1: inflammatory response (Additional file 2: Figure E1)

CPT1B

Lipid transport

Regulated by TNF (Table 3)

CXCL1 (secreted)

Chemoattractant for neutrophils – Tumor growth

Target molecule (Table 2); Regulated by TNF, IL1B, OSM, IL6, NFkB, MYD88, JUN, RELA (Table 3); Networks: immune response, remodeling and lipid metabolism (Figs. 2, 3, 4)

CXCL8 (secreted)

Neutrophil attraction and activation

Target molecule (Table 2); Regulated by TNF, IL1B, OSM, IL6, NFkB, MYD88, Akt, ERK, JUN, RELA, STA1, STA3 (Table 3); Networks: immune response, remodeling and lipid metabolism (Figs. 2, 3, 4)

CYP1A1

Cholesterol and lipid synthesis

Target molecule (Table 2); Regulated by TNF, IL1B, ERK, RELA (Table 3); Networks: remodeling and lipid metabolism (Figs. 3, 4)

EGLN2 (egl-9 family hypoxia-inducible factor 2)

Hypoxia tolerance-Tumor proliferation

FLRT1

Fibroblast growth factor

Regulated by tretinoin (Additional file 4: Table E3)

FOXD2

Somatogenesis

FOXD3

Promotes development of neural cells

Regulated by tretinoin (Additional file 4: Table E3); Networks: immune response (Fig. 2)

FRMPD1 (FERM and PDZ domain containing 1)

Stabilizes membrane-bound GPSM1

GNG3

Gamma subunit of guanine nucleotide binding proteins

ICAM1

Leukocyte migration-Rhinovirus receptor

Target molecule (Table 2); Regulated by TNF, IL1B, OSM, IL6, NFkB, MYD88, ERK, JUN, RELA, STAT1, STAT3 (Table 3) Networks: immune response, remodeling (Figs. 2,3)

IGSF6

IL6 (secreted)

Induces inflammatory response-Insulin resistance-Nerve cells differentiation

Target molecule (Table 2); Regulated by TNF, IL1B, IL6, NFkB, MYD88, Akt, ERK, JUN, RELA, STAT1, STAT3 (Table 3) Networks: immune response, remodeling, lipid metabolism (Figs. 2, 3, 4)

KLKB1 (kallikrein B, plasma (Fletcher factor) 1

Blood coagulation-Inflammation

KRT36 (keratin 36, type I)

Type I hair keratin

MYO1H (myosin IH)

Actin based intracellular movement

NATD1 (N-acetyltransferase domain containing 1)

NFKBIZ

LPS induced-Increases IL-6 production

Target molecule (Table 2); Regulated by TNF, IL1B, MYD88, ERK, JUN, STAT3 (Table 3)

NUP210

Part of nuclear pore complex

OR51B5

PALD1

PCBP3 (poly(rC) binding protein 3)

RNA-binding proteins

PRODH (proline dehydrogenase (oxidase) 1)

Mitochondrial proline degradation

Network 1: inflammation, neurological disease (Additional file 2: Figure E1)

PYHIN1 (pyrin and HIN domain family, member 1)

Promote ubiquitination- IFN-induced

Network 2: cell trafficking (Additional file 8: Figure E2)

SOX7

Represses Wnt/beta-catenin pathway

SYNDIG1

IFN-induced- Synaptogenesis

TTC6 (Tetratricopeptide repeat protein 6)

UCN2 (secreted)

Homeostasis after stress

Networks: lipid metabolism

ZC3H12A

CCL2-induced- Cell death- mRNA decay (IL-6 and IL12B)- Inhibits miRNAPromote IL-4-induced M2- Increase glial differentiation

Target molecule (Table 2); Regulated by TNF, IL1B, NFkB (Table 3); Networks: remodeling (Fig. 3)

ZMYND15

Spermatogenesis- transcriptional repressor via histone deacetylase