Background
Methods
Selventa Knowledgebase (SK)
Subnetwork | Total edges | Edges >1 evidence annotated with vascular context | Vascular edges/Total (%) |
---|---|---|---|
Endothelial Cell Activation | 407 | 238 | 58 |
Smooth Muscle Cell Activation | 179 | 78 | 44 |
Plaque Destabilization | 494 | 144 | 29 |
Endothelial Cell – Monocyte Interaction | 112 | 27 | 24 |
Foam Cell Formation | 285 | 27 | 9 |
Platelet Activation | 179 | 10 | 6 |
RCR-based HYP generation process
V-IPN construction: model structure and boundaries
Gene expression datasets used for V-IPN construction and evaluation
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 |
Gene expression datasets used as negative controls
Dataset name | Dataset ID | PubMed ID | Species | Experimental context | Tissue/cell type | Perturbation | Time point | Independent endpoint | Control |
---|---|---|---|---|---|---|---|---|---|
Hs_NHBE_CDKinh_rel_vs_blk_8 h
| E-MTAB-1272 | 23926424 | Hs |
in vitro
| NHBE | Exposure to CDK4/6 inhibitor | 24 exposure + 8 h after removal of inhibitor | FACS, cell cycle analysis | Untreated |
Hs_MVEC-C_hpx_vs_ct_24 h
| GSE11341 | 18469115 | Hs |
In vitro
| Primary cardiac microvascular ECs | 24 h hypoxia (1% O2) | Normoxia (21% O2) | ||
Hs_MVEC-L_hpx_vs_ct_24 h
| GSE11341 | 18469115 | Hs |
In vitro
| Primary human pulmonary microvascular ECs | 24 h hypoxia (1% O2) | Normoxia (21% O2) | ||
Hs_JurkT_ars_vs_ct
| GSE46909 | 23824090 | Hs |
In vitro
| Jurkat T cells | Arsenic trioxide 3 μM | 6 h exposure | Untreated |
Calculation of coverage and odds ratio
CS generation and ApoE-/- mice exposure
Results
V-IPN construction and biological integration: description of modular framework and boundaries
Assessment of V-IPN subnetwork-level HYP coverage
Test datasets
Dataset name | Dataset ID | N° of state changes (SC) | N°of HYPs in dataset | NoHYPs overlapping withEC activation
| N° HYPs overlapping withplatelet activation
| N° HYPs overlapping withEC-monocyte interaction
| N° HYPs overlapping withfoam cell formation
| N° HYPs O/L with SMC Activation
| N° HYPs O/L with Plaque Destabilization
| N° HYPs O/L with V-IPN | |
---|---|---|---|---|---|---|---|---|---|---|---|
Total N°
of possible HYPs in each subnetwork for human/mouse
| 2410/ 2354 | 155/149 | 59/55 | 30/27 | 118/113 | 88/84 | 104/102 | 340*/334 | |||
Mouse
| Mm_Ao_78w_ApoE_vs_wt | GSE10000 | 3872 | 449 | 59 | 11 | 13 | 42 | 32 | 43 | 110 |
Mm_Ao_16w_ApoE_CS_vs_sham | E-MTAB-1696 | 1928 | 245 | 24 | 8 | 4 | 23 | 19 | 18 | 52 | |
Human
| Hs_EC_GFP_oxLDL_vs_ct | GSE13139 | 398 | 152 | 16 | 4 | 4 | 16 | 9 | 14 | 31 |
Hs_EC_LOX1_oxLDL_vs_ct | GSE13139 | 752 | 224 | 30 | 8 | 8 | 21 | 16 | 21 | 52 | |
Hs_EC_oxPAP_vs_ct | GSE20060 | 609 | 309 | 45 | 12 | 8 | 21 | 23 | 27 | 77 | |
Hs_athCA_vs_ctIMA | GSE40231 | 3643 | 309 | 42 | 17 | 11 | 36 | 20 | 37 | 80 | |
Hs_NHBE_CDKinh_rel_vs_blk_8h | E-MTAB-1272 | 1655 | 296 | 27 | 5 | 7 | 19 | 18 | 14 | 53 | |
Hs_MVEC-C_hpx_vs_ct_24h | GSE11341 | 459 | 192 | 27 | 8 | 4 | 16 | 16 | 18 | 48 | |
Hs_MVEC-L_hpx_vs_ct_24h | GSE11341 | 504 | 198 | 22 | 4 | 4 | 15 | 13 | 14 | 42 | |
Hs_JurkT_ars_vs_ct | GSE46909 | 2381 | 157 | 15 | 5 | 3 | 3 | 9 | 8 | 31 |
Negative Control Datasets
HYP scoring and HYP directionality
V-IPN evaluation of preclinical data translatability
V-IPN coverage of predicted HYPs from human in vitro datasets
V-IPN coverage of predicted HYPs from human and murine in vivo datasets
Mm_Ao_16w_ApoE_CS_vs_sham
|
Mm_Ao_78w_ApoE_vs_wt
|
Hs_athCA_vs_ctIMA
| No of HYPs |
EC activation
|
Platelet activation
|
EC-monocyte interaction
|
Foam cell formation
|
SMC activation
|
Plaque destabilization
|
---|---|---|---|---|---|---|---|---|---|
X | X | X | 18 | 11 (7) | 3 (5) | 2 (7) | 8 (7) | 9 (10) | 9 (9) |
X | X | - | 8 | 2 (1) | 0 (0) | 0 (0) | 4 (3) | 3 (3) | 1 (1) |
X | - | X | 6 | 2 (1) | 0 (0) | 2 (7) | 3 (3) | 2 (2) | 4 (4) |
- | X | X | 32 | 18 (12) | 6 (10) | 5 (17) | 15 (13) | 4 (5) | 16 (16) |
X | - | - | 20 | 9 (6) | 5 (8) | 0 (0) | 8 (7) | 5 (6) | 4 (4) |
- | X | - | 51 | 28 (18) | 2 (3) | 6 (21) | 15 (13) | 16 (18) | 17 (17) |
- | - | X | 24 | 11 (7) | 8 (14) | 2 (7) | 10 (8) | 5 (6) | 8 (8) |
- | - | - | 583 | 73 (47) | 36 (61) | 12 (41) | 55 (47) | 43 (49) | 44 (43) |