Name
Title | ||
|---|---|---|
Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data |
Abstract | ||
|---|---|---|
Motivation: High-throughput technologies have facilitated the acquisition of large genomics and proteomics datasets. How- ever, these data provide snapshots of cellular behavior, rather than help us reveal causal relations. Here, we propose how these technologies can be utilized to infer the topology and strengths of connections among genes, proteins and meta- bolites by monitoring time-dependent responses of cellular networks to experimental interventions. Results: We demonstrate that all connections leading to a given network node, e.g. to a particular gene, can be deduced from responses to perturbations none of which directly influ- ences that node, e.g. using strains with knock-outs to other genes. To infer all interactions from stationary data, each node should be perturbed separately or in combination with other nodes. Monitoring time series provides richer informa- tion and does not require perturbations to all nodes. Overall, the methods we propose are capable of deducing and quan- tifying functional interactions within and across cellular gene, signaling and metabolic networks. |
Year | DOI | Venue |
|---|---|---|
2004 | 10.1093/bioinformatics/bth173 | Bioinformatics |
Keywords | Field | DocType |
selection,gene duplication,time series,molecular evolution,gene expression,cellular network,high throughput,metabolic network | Data mining,Proteomics,Computer science,Molecular evolution,Node (networking),Network architecture,Stationary process,Genomics,Cellular network,Bioinformatics,Snapshot (computer storage) | Journal |
Volume | Issue | ISSN |
20 | 12 | 1367-4803 |
Citations | PageRank | References |
44 | 6.69 | 7 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Eduardo D. Sontag | 1 | 3134 | 781.88 |
| Anatoly Kiyatkin | 2 | 50 | 7.32 |
| Boris N Kholodenko | 3 | 111 | 12.65 |