Pajek— Analysis and Visualization of Large Networks

Batagelj, Vladimir; Mrvar, Andrej

doi:10.1007/3-540-45848-4_54

Cited by 435 publications

(385 citation statements)

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“…The joints were at relatively large heights and reflected that the corresponding changes in transcript levels were not identical but similar among pairs and groups of AtSBT genes. For further analysis, we visualized as a network significant, Bonferroni corrected [48] correlations among the AtSBT genes using the Pajek software [49] (Figure 4B). In conjunction with the cluster tree drawn on the basis of the common co-responses (Figure 4B), the obtained AtSBT network revealed two AtSBT cliques, where each gene member showed significant correlation to the other members.…”

Section: Resultsmentioning

confidence: 99%

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Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family

et al. 2005

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The gene family of subtilisin-like serine proteases (subtilases) in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative bioinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co-regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i) control of development, (ii) protein turnover, and (iii) action as downstream components of signalling cascades. Supplemental material is available in the Plant Subtilase Database (PSDB) (http://csbdb.mpimp-golm.mpg.de/psdb.html) , as well as from the CSB.DB (http://csbdb.mpimp-golm.mpg.de).

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Section: Resultsmentioning

confidence: 99%

“…HCA was performed as mentioned above. Visualization of significant associations was done with the software Pajek [49]. The multiple comparison performed required the adjustment of α to accept significant associations, which was done by application of the Bonferroni correction α′ = α/k.…”

Section: Methodsmentioning

confidence: 99%

Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family

et al. 2005

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“…Most analyses in this paper were performed with MATLAB R2011b (The MathWorks, Inc., Natick, MA). Network visualization was achieved with the programs Pajek [19] and Gephi [20]. …”

Section: Methodsmentioning

confidence: 99%

Next-generation sequencing reveals large connected networks of intra-host HCV variants

et al. 2014

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BackgroundNext-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.ResultsIntra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient.The distance between any two variants calculated over the component correlated strongly with nucleotide distances (r = 0.9499; p = 0.0001), a better correlation than the one obtained with Neighbour-Joining trees (r = 0.7624; p = 0.0001). In each patient, components were well separated, with the average distance between (6.53%) being 10 times greater than within each component (0.68%). The ratio of nonsynonymous to synonymous changes was calculated and some patients (6.9%) showed a mixture of networks under strong negative and positive selection. All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes. In vitro sampling showed that 93.02% of components present in the original sample were also found in experimental replicas, with 81.6% of reads found in both. When syringe-sharing transmission events were simulated, 91.2% of all simulated transmission events seeded all components present in the source.ConclusionsMost intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.

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“…The identification of subnetworks was undertaken through the mapping of simple ‘line islands’ (Batagelj & Mrvar 1998, 2002; Batagelj & Mrvar 2003; de Nooy et al . 2005).…”

Section: Methodsmentioning

confidence: 99%

Climatic similarity and biological exchange in the worldwide airline transportation network

Tatem

Hay

2007

Proc. R. Soc. B.

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Recent increases in the rates of biological invasion and spread of infectious diseases have been linked to the continued expansion of the worldwide airline transportation network (WAN). Here, the global structure of the WAN is analysed in terms of climatic similarity to illuminate the risk of deliberate or accidental movements of climatically sensitive organisms around the world. From over 44,000 flight routes, we show, for each month of an average year, (i) those scheduled routes that link the most spatially distant but climatically similar airports, (ii) the climatically best-connected airports, and (iii) clusters of airports with similar climatic features. The way in which traffic volumes alter these findings is also examined. Climatic similarity across the WAN is skewed (most geographically close airports are climatically similar) but heavy-tailed (there are considerable numbers of geographically distant but climatically similar airports), with climate similarity highest in the June-August period, matching the annual peak in air traffic. Climatically matched, geographically distant airports form subnetworks within the WAN that change throughout the year. Further, the incorporation of passenger and freight traffic data highlight at greater risk of invasion those airports that are climatically well connected by numerous high capacity routes.

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Pajek— Analysis and Visualization of Large Networks

Cited by 435 publications

References 4 publications

Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family

Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family

Next-generation sequencing reveals large connected networks of intra-host HCV variants

Climatic similarity and biological exchange in the worldwide airline transportation network

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