Optimization and Analysis of Seriation Algorithm for Ordering Protein Networks

Kuentzer, Felipe A.; Pereira, Alexandre S.; Amory, Alexandre M.; Perrone, Gabriel C.; Silva, Samoel R.M.; Dinis, J.; Almeida, Rita Maria Cunha de

doi:10.1109/bibe.2014.43

Cited by 3 publications

(1 citation statement)

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“…Such clustering methods are mathematically arbitrary, thus have little a priori biological basis. This study uses matrix seriation ( 18 ), a method that reorders a matrix of gene–gene interaction into a cyclical arrangement, if one exists, instead of a clustered arrangement made by the currently popular clustering algorithms. The seriation method is inspired by the famous ‘Traveling Salesman Problem’ ( 19 ) to calculate an optimal cycle among the genetic interaction data, with the assumption that the optimal arrangement likely coincides with an optimum temporal biological process cycle.…”

Section: Introductionmentioning

confidence: 99%

The interplay between chromosome stability and cell cycle control explored through gene–gene interaction and computational simulation

Frumkin

Patra

Sevold

et al. 2016

Nucleic Acids Research

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Chromosome stability models are usually qualitative models derived from molecular-genetic mechanisms for DNA repair, DNA synthesis, and cell division. While qualitative models are informative, they are also challenging to reformulate as precise quantitative models. In this report we explore how (A) laboratory experiments, (B) quantitative simulation, and (C) seriation algorithms can inform models of chromosome stability. Laboratory experiments were used to identify 19 genes that when over-expressed cause chromosome instability in the yeast Saccharomyces cerevisiae. To better understand the molecular mechanisms by which these genes act, we explored their genetic interactions with 18 deletion mutations known to cause chromosome instability. Quantitative simulations based on a mathematical model of the cell cycle were used to predict the consequences of several genetic interactions. These simulations lead us to suspect that the chromosome instability genes cause cell-cycle perturbations. Cell-cycle involvement was confirmed using a seriation algorithm, which was used to analyze the genetic interaction matrix to reveal an underlying cyclical pattern. The seriation algorithm searched over 1014 possible arrangements of rows and columns to find one optimal arrangement, which correctly reflects events during cell cycle phases. To conclude, we illustrate how the molecular mechanisms behind these cell cycle events are consistent with established molecular interaction maps.

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Section: Introductionmentioning

confidence: 99%

The interplay between chromosome stability and cell cycle control explored through gene–gene interaction and computational simulation

Frumkin

Patra

Sevold

et al. 2016

Nucleic Acids Research

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Modeling Chromosome Maintenance as a Property of Cell Cycle inSaccharomyces cerevisiae

Frumkin

Patra

Sevold

et al. 2016

Preprint

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A healthy cell must maintain chromosome integrity during each phase of the cell cycle. Yet during the cell cycle, defects in DNA repair, DNA synthesis, and chromosome transmission can cause chromosome instability. Here, we build a cyclical model for chromosome maintenance by assaying the genetic interactions of pairs of genes that each normally functions to maintain chromosomes. First, we confirm that 19 genes affect chromosome maintenance by overexpressing the respective genes using an assay for chromosome instability. We then introduce plasmids containing these 19 genes into 18 deletion mutant strains each of which is known to cause chromosome maintenance defect. By conditionally overexpressing each of the 19 genes in each of the 18 deletion strains, we observe 34 cases of synthetic dosage lethality, 58 of synthetic dosage sickness, and 26 of suppression (out of 349 combinations tested). Ordinarily, given a large matrix of genetic interactions, it is computationally intractable (and NP hard) to compute all permutations of the arrangements of the rows and columns, which is necessary for finding an optimum arragement of entries for a given pattern of functional significance. Here, using our small yet dense matrix we rearrange the matrix into an optimal cycle. By optimally reordering the matrix representation of these genetic interactions using integer linear programming, we find that the optimal order of the functions of the genes approximates the temporal order of processes during the yeast cell cycle. To further validate this theoretical approach, we computed in silico genetic interactions derived from a predetermined cyclical model and confirmed that the predicted cycle was consistent. These results suggest that matrices from other genetic experiments could be computationally rearranged using this method to reveal an underlying cycle that is biological meaningful. 10/15 11/15

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A Module-Based Approach for Evaluating Differential Genome-Wide Expression Profiles

Dias¹,

Alves

Commes

2016

2016 5th Brazilian Conference on Intelligent Systems (BRACIS)

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Optimization and Analysis of Seriation Algorithm for Ordering Protein Networks

Cited by 3 publications

References 20 publications

The interplay between chromosome stability and cell cycle control explored through gene–gene interaction and computational simulation

The interplay between chromosome stability and cell cycle control explored through gene–gene interaction and computational simulation

Modeling Chromosome Maintenance as a Property of Cell Cycle inSaccharomyces cerevisiae

A Module-Based Approach for Evaluating Differential Genome-Wide Expression Profiles

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