Navigation Links
Assortativity signatures of transcription factor networks contribute to robustness
Date:8/29/2014

Dartmouth researchers explored the type and number of connections in transcription factor networks (TFNs) to evaluate the role assortativity plays on robustness in a study published in PLOS Computational Biology in August. The study found that the assortativity signature contributes to a network's resilience against mutations.

"In simulations, it seems that varying the out-out assortativity of TFN models has a greater effect on robustness than varying any of the other three types of assortativity," said Dov A. Pechenick, PhD, lead author and former researcher at the Computational Genetics Laboratory at Dartmouth College, Hanover, NH. "We determined this by varying all four types of assortativity in the signature and then measuring robustness."

Transcription factors (TFs) are proteins that initiate and regulate the expression of a gene. To achieve their genetic mission, TFs also regulate one another's expression. Individual TFs connect to each other through connections that point in or out, forming a network. The direction of the coupling indicates regulatory control; an outbound connection by one TF stipulates its control over another, whereby it turns that TF on or off with respect to gene expression.

Many such connected pairings occur in a network, and their types determine a network's assortativity, which measures whether these pairings tend to occur between TFs that have similar numbers of connections. For example, when TFs in a pairing are likely to possess similar numbers of outgoing connections, out-out assortativity is high. If they are likely to possess very different numbers of incoming connections, in-in assortativity is low. Taken together, measures for the different kinds of assortativity create a signature. According to Pechenick, "There are four types of assortativity in directed networks, and the assortativity signature is a way of looking at all four at once."

Pechenick and his Dartmouth co-authors evaluated the assortativity signatures in published TFNs of 41 distinct human cell and tissue types and found that an above average number of connected TFs had similar numbers of outgoing connections (high out-out assortativity). Furthermore, this property, more so than the other three types of assortativity, seemed to be a predictor of robustness.

"Robustness is a measure of how resilient an overall pattern of TF gene expression is over time when confronted with mutations in the regulatory instructions of these TFs. If mutations tend to change the pattern, then robustness is low. If mutations tend to have no effect on the pattern, then robustness is high," said Pechenick.

This Dartmouth study was the first to look at the assortativity signatures of TFNs and their impact on robustness. "Results suggest that measuring the assortativity signature of a TFN can tell you something about its robustness," said Pechenick. "For researchers that wish to understand and simulate biological networks, these results indicate the importance of considering assortativity."


'/>"/>

Contact: Donna Dubuc
Donna.M.Dubuc@Dartmouth.edu
603-653-3615
The Geisel School of Medicine at Dartmouth
Source:Eurekalert

Related biology news :

1. Epigenetic signatures direct the repair potential of reprogrammed cells
2. Biosignatures distinguish between tuberculosis and sarcoidosis
3. Oncogenic signatures mapped in TCGA a guide for the development of personalized therapy
4. Signatures of selection inscribed on poplar genomes
5. Study demonstrates cells can acquire new functions through transcriptional regulatory network
6. Transcription factor Lyl-1 critical in producing early T-cell progenitors
7. NIH backs Rice University study of delay in gene transcription networks
8. Stay-at-home transcription factor prevents neurodegeneration
9. FASEB SRC announces: Mechanism and Regulation of Prokaryotic Transcription Conference
10. Transcription factor may protect against hepatic injury caused by hepatitis C and alcohol
11. System-wide analyses have underestimated the importance of transcription in animals
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:4/15/2016)... 15, 2016 Research and ... Biometrics Market 2016-2020,"  report to their offering.  , ... , ,The global gait biometrics market is expected ... the period 2016-2020. Gait analysis generates ... be used to compute factors that are not ...
(Date:3/31/2016)...  Genomics firm Nabsys has completed a financial  restructuring ... , M.D., who returned to the company in October ... team, including Chief Technology Officer, John Oliver , ... and Vice President of Software and Informatics, Michael ... Dr. Bready served as CEO of Nabsys from 2005-2014 ...
(Date:3/22/2016)... Ontario , PROVO and ... Newborn Screening Ontario (NSO), which operates the ... for molecular testing, and Tute Genomics and UNIConnect, ... management technology respectively, today announced the launch of a ... next-generation sequencing (NGS) testing panel. NSO ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... , June 27, 2016  Liquid Biotech ... announced the funding of a Sponsored Research Agreement ... circulating tumor cells (CTCs) from cancer patients.  The ... in CTC levels correlate with clinical outcomes in ... These data will then be employed to support ...
(Date:6/24/2016)... ... ... Researchers at the Universita Politecnica delle Marche in Ancona combed medical journal articles ... findings are the subject of a new article on the Surviving Mesothelioma website. ... blood, lung fluid or tissue of mesothelioma patients that can help point doctors to ...
(Date:6/23/2016)... June 23, 2016 A person commits a crime, ... scene to track the criminal down. An outbreak ... and Drug Administration (FDA) uses DNA evidence to track down ... Sound far-fetched? It,s not. The FDA has increasingly used ... investigations of foodborne illnesses. Put as simply as possible, whole ...
(Date:6/23/2016)... 2016   EpiBiome , a precision microbiome engineering ... debt financing from Silicon Valley Bank (SVB). The financing ... advance its drug development efforts, as well as purchase ... "SVB has been an incredible strategic partner to us ... bank would provide," said Dr. Aeron Tynes Hammack ...
Breaking Biology Technology: