Name
Title | ||
|---|---|---|
Inferring genome-wide functional modulatory network: a case study on NF-κB/RelA transcription factor. |
Abstract | ||
|---|---|---|
How different pathways lead to the activation of a specific transcription factor (TF) with specific effects is not fully understood. We model context-specific transcriptional regulation as a modulatory network: triplets composed of a TF, target gene, and modulator. Modulators usually affect the activity of a specific TF at the posttranscriptional level in a target gene-specific action mode. This action may be classified as enhancement, attenuation, or inversion of either activation or inhibition. As a case study, we inferred, from a large collection of expression profiles, all potential modulations of NF-kappa B/RelA. The predicted modulators include many proteins previously not reported as physically binding to RelA but with relevant functions, such as RNA processing, cell cycle, mitochondrion, ubiquitin-dependent proteolysis, and chromatin modification. Modulators from different processes exert specific prevalent action modes on distinct pathways. Modulators from noncoding RNA, RNA-binding proteins, TFs, and kinases modulate the NF-kappa B/RelA activity with specific action modes consistent with their molecular functions and modulation level. The modulatory networks of NF-kappa B/RelA in the context epithelial-mesenchymal transition (EMT) and burn injury have different modulators, including those involved in extracellular matrix (FBN1), cytoskeletal regulation (ACTN1), and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long intergenic nonprotein coding RNA, and tumor suppression (FOXP1) for EMT, and TXNIP, GAPDH, PKM2, IFIT5, LDHA, NID1, and TPP1 for burn injury. |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1089/cmb.2014.0299 | JOURNAL OF COMPUTATIONAL BIOLOGY |
Keywords | DocType | Volume |
modulatory network,integrative probabilistic model,NF-kappa B,transcription factor,modulator | Journal | 22.0 |
Issue | ISSN | Citations |
4 | 1066-5277 | 2 |
PageRank | References | Authors |
0.52 | 1 | 4 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Xueling Li | 1 | 74 | 5.80 |
| Min Zhu | 2 | 5 | 1.96 |
| Allan R. Brasier | 3 | 15 | 2.95 |
| Andrzej Kudlicki | 4 | 5 | 2.00 |