A travel guide to Cytoscape plugins

Saito, Rintaro; Smoot, Michael; Ono, Keiichiro; Ruscheinski, Johannes; Wang, Pengliang; Lotia, Samad; Pico, Alexander R.; Bader, Gary D.; Ideker, Trey

doi:10.1038/nmeth.2212

Cited by 1,306 publications

(1,035 citation statements)

References 64 publications

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“…The network was generated using the CoNet plugin for Cytoscape on the basis of the nonparametric Spearman correlation coefficients with a minimal cutoff threshold of r ¼ 0.6 (Po0.01, Bonferroni corrected) 38,39 . We present correlation data for OTUs that were detected in at least 50% of the gut samples (n ¼ 13 for black vultures, n ¼ 11 for turkey vultures).…”

Section: Methodsmentioning

confidence: 99%

The microbiome of New World vultures

et al. 2014

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Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture's gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures and their bacteria to their food source, exemplifying a specialized host-microbial alliance.

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Section: Methodsmentioning

confidence: 99%

The microbiome of New World vultures

et al. 2014

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“…The complete Oropetium-Arabidopsis orthologue list was then filtered to focus on genes with functional data in the STRING v9.1 global Arabidopsis protein interaction network 53 . Gene expression patterns and duplicated genes (tandem and wholegenome duplicates) were mapped onto this network using Cytoscape v3.1.1 54 to identify clusters of co-expressed and interacting duplicate genes, respectively (Extended Data Fig. 6).…”

Section: Methodsmentioning

confidence: 99%

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

VanBuren

Bryant

Edger

et al. 2015

Nature

288

271

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Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly 1 . The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE) 2 . Here we report the whole-genome sequencing and assembly of the desiccationtolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.The genomes of Arabidopsis 3 , rice 4 , poplar, grape and Sorghum 5 were first sequenced using high-quality and reiterative Sanger-based approaches producing a series of 'gold standard' reference genomes. The advent of next-generation sequencing (NGS) technologies reduced costs of sequencing substantially, which has enabled sequencing of over 100 plant genomes 1 . The quality of plant genome assemblies depends on genome size, ploidy, heterozygosity and sequence coverage, but most NGS-based genomes have on the order of tens of thousands of short contigs distributed in thousands of scaffolds. The short read lengths of NGS, inherent biases and non-random sequencing errors have resulted in highly fragmented draft genome assemblies that are not complete, which means they are missing biologically meaningful sequences including entire genes, regulatory regions, transposable elements, centromeres, telomeres and haplotype-specific structural variations. It is becoming clear from ENCODE projects that complete genomes are needed to better understand the importance of the non-coding regions of genomes 2 .More than 40% of calories consumed by humans are derived from grasses, and the grass family (Poaceae) is arguably the most important plant family with regard to global food security 6 . The size and complexity of most grass genomes has challenged progress in gene discovery and comparative genomics, although draft genomes are now available for most agriculturally important grasses 1 . The largest genome assemblies, such as maize (2,300 megabases (Mb)) 7 , barley (5,100 Mb) 8 and wheat (hexaploid, 1...

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“…We provide tools for navigation in the domain and motif networks by integrating Cytoscape (38) and PyMOL (39). To visualize our networks, download the Cytoscape files describing them at http://cs.haifa.ac.il/∼trachel/domain_motif_networks/.…”

Section: The Motif Network Reveals the Ubiquitous Reuse Of Motifs In mentioning

confidence: 99%

Global view of the protein universe

Nepomnyachiy

Ben‐Tal

Kolodny

2014

Proc. Natl. Acad. Sci. U.S.A.

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To explore protein space from a global perspective, we consider 9,710 SCOP (Structural Classification of Proteins) domains with up to 70% sequence identity and present all similarities among them as networks: In the "domain network," nodes represent domains, and edges connect domains that share "motifs," i.e., significantly sized segments of similar sequence and structure. We explore the dependence of the network on the thresholds that define the evolutionary relatedness of the domains. At excessively strict thresholds the network falls apart completely; for very lax thresholds, there are network paths between virtually all domains. Interestingly, at intermediate thresholds the network constitutes two regions that can be described as "continuous" versus "discrete." The continuous region comprises a large connected component, dominated by domains with alternating alpha and beta elements, and the discrete region includes the rest of the domains in isolated islands, each generally corresponding to a fold. We also construct the "motif network," in which nodes represent recurring motifs, and edges connect motifs that appear in the same domain. This network also features a large and highly connected component of motifs that originate from domains with alternating alpha/ beta elements (and some all-alpha domains), and smaller isolated islands. Indeed, the motif network suggests that nature reuses such motifs extensively. The networks suggest evolutionary paths between domains and give hints about protein evolution and the underlying biophysics. They provide natural means of organizing protein space, and could be useful for the development of strategies for protein search and design.protein cooccurrence networks | protein similarity networks H ow are proteins related to each other? Which physicochemical considerations affect protein evolution and how? A global view of the protein universe may shed light on these fundamental questions. It could also suggest new strategies for protein search and design (1-3). However, forming a global picture of the protein universe is difficult because we have to piece it together from the many local glimpses that our empirical data and computational tools provide. In other words, a global picture needs to portray the relationships among all proteins, yet we only have evidence of such relationships among several proteins, based on the similarity between their sequences, structures, and functions. The considerable size of the Protein Data Bank (4) also complicates this task.In particular, an intensely debated question is whether protein space is "discrete" or "continuous" (2, 3, 5-10). These terms are loosely defined. Discrete implies that the global picture consists of separate, island-like, structural entities. In the hierarchical protein domains Structural Classification of Proteins (SCOP) (11) these entities are termed "folds," and in the CATH database (12) they are called "topologies." Alternatively, "continuous" implies that the space between these entities is generally populated by...

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A travel guide to Cytoscape plugins

Cited by 1,306 publications

References 64 publications

The microbiome of New World vultures

The microbiome of New World vultures

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

Global view of the protein universe

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