NetPert Twist1 Atlas
Drug-target prioritisation with network response functions (Perrone et al., PLOS Comp. Biol. 2024) — run on the IID mouse interactome + TRRUST regulatory network, Twist1 RNA-seq responses, and dissemination assays. GitHub repo
Start here: read the full report —
23 sections, one page each: the Twist1 run, methods, benchmarks, robustness checks, the sortable gene explorer,
data tables and scorecard. Highlights continue below.
Network: 17,191 genes / 1,891,745 directed edges (IID PPI + TRRUST v2).
Driver: Twist1. Responses: 168/182 DE genes in-network (14 absent from the interactome).
Method: dense NetPert (nt=16, r=0.5) on a 1,200-gene Twist1-centered subnetwork; conservation check 1.99e-15.
Betweenness run on the full 17k-gene network. Full table: geneRankings_real.tsv
Top-20 NetPert intermediates
| # | Gene | Weight | BC rank | Repurposing compounds |
|---|---|---|---|---|
| 1 | Pdgfra | 2.13e-02 | 3 | AC-710, BMS-536924, CP-673451 |
| 2 | Htt | 1.80e-02 | 1 | — |
| 3 | Tp53 | 1.76e-02 | 4 | — |
| 4 | Ctnnb1 | 1.53e-02 | 6 | CCT-031374, ICG-001, PNU-74654 |
| 5 | Cdh1 | 1.51e-02 | 5 | — |
| 6 | Zranb1 | 1.43e-02 | 2 | — |
| 7 | Vim | 1.37e-02 | 7 | — |
| 8 | Ppia | 1.36e-02 | 27 | L-proline, TMN-355, cyclosporin-A |
| 9 | Stat3 | 1.28e-02 | 10 | APcK-110, STAT3-inhibitor-VI, WP1066 |
| 10 | Clu | 1.28e-02 | 20 | — |
| 11 | Stub1 | 1.26e-02 | 25 | — |
| 12 | Nfkb1 | 1.25e-02 | 17 | SP-100030, andrographolide, arglabin |
| 13 | Ep300 | 1.15e-02 | 14 | C646, I-CBP-112, SGC-CBP30 |
| 14 | Sox2 | 1.14e-02 | 8 | — |
| 15 | Col2a1 | 1.08e-02 | 9 | — |
| 16 | Rela | 1.08e-02 | 19 | BAY-11-7082, acetylcysteine, bortezomib |
| 17 | Kif23 | 1.07e-02 | 21 | — |
| 18 | Hif1a | 1.04e-02 | 40 | 2-methoxyestradiol, YC-1, acriflavine |
| 19 | Hdac6 | 1.02e-02 | 15 | ACY-1215, belinostat, dacinostat |
| 20 | H4c1 | 1.02e-02 | 12 | — |
Figures
Highlights below — the full figure gallery holds the grouped visuals, including multi-panel dashboards and report-style plots computed on the network.
Contact
Sources: Perrone et al. 2024 (doi:10.1371/journal.pcbi.1012195) · code ref joelbaderlab/netpert_v1 · IID · TRRUST v2 · EwaldLab 2019_Prkd1 (Georgess et al. 2019) · Drug Repurposing Hub 2020-03-24 · MGI homology.