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Table 2 Datasets analyzed by RCR for V-IPN augmentation and evaluation

From: A vascular biology network model focused on inflammatory processes to investigate atherogenesis and plaque instability

  Dataset name Dataset ID PubMed ID Species Experimental context Tissue/cell type Perturbation Timepoint Independent endpoint Control
Model Building Datasets Hs_EC_oxPAP_vs_PAP GSE29903 16912112 (Gargalovic, 2006) Hs in vitro HAECs oxPAPC (40 μg/ml) 4 h IL8 induction PAPC
(40 μg/ml)
Mm_Ao_32w_ApoE_vs_wt GSE2372 19139167 (Grabner, 2009) Mm in vivo Aorta ApoE-/- 32 wk of age Aortic morphometry, IHC, FACS Wild-type mice (C57BL/6 J)
Mm_Ao_78w_ApoE_vs_wt GSE10000 78 wk of age
Test Datasets Hs_EC_GFP_oxLDL_vs_ct GSE13139 19279231 (Mattaliano, 2009) Hs in vitro HAECs (cell line) GFP overexp oxLDL 24 h IL8 induction Untreated
Hs_EC_LOX1_oxLDL_vs_ct LOX-1 overexp
Hs_EC_oxPAP_vs_ct GSE20060 20170901 (Romanoski, 2010) Hs in vitro Primary HAECs Ox-PAPC (40 μg/ml) 4 h eQTL analysis Untreated
Hs_athCA_vs_ctIMA GSE40231 19997623 (Hagg, 2009) Hs in vivo Coronary artery Atherosclerotic lesions 66 ± 8 yr of age Angiography, blood cytokines Paired unaffected artery (IMA)
  Mm_Ao_16w_ApoE_CS_vs_sham E-MTAB-1696 - Mm in vivo (ApoE-/-) Aorta CS exposure 13-16 wk of age; 30 d exposure Lipoprotein profile Fresh air exposure
  1. ECs: endothelial cells; HAECs: human aortic endothelial cells (ECs); GFP: green fluorescent protein; OxPAPC: oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine; oxLDL: oxidized low density lipoprotein; IHS: immunohistochemistry; FACS: fluorescence-activated cell sorting; eQTL: expression quantitative trait loci; Hs: homo sapiens; IMA: internal mammary artery; Mm: mus musculus, MVECs: microvascular endothelial cells; h: hours; d: days; wk: weeks; yr: years.