Circos + Chromatin Topology

An organism's B and T lymphocytes — cells that are part of the immune system — continually develop new receptors specific to new threats to the immune system.

These receptor loci are organized into distinct regions that contain multiple variable (V), diversity (D), and/or joining (J) and constant (C) coding elements that are scattered across large genomic regions.

Bossen et al. review the relationship between epigenetics and chromatin and its effect on the diversity of receptors.

Bossen C, Mansson R, Murre C 2012 Chromatin topology and the regulation of antigen receptor assembly Annual review of immunology 30:337-356.

// circos-chromatin

Circos fruit salad

Circos demonstrates sequence synteny between genomes of peach, apple and strawberry.

Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera.

Jung S, Cestaro A, Troggio M et al. 2012 Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies BMC Genomics 13:129.

// circos-rosaceae

Circos visualizes a 18.2 Gb metagenome

The genomes of all members in an ecosystem compose the system's metagenome.

In A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal, Albertsen et al. use Circos to compare the genome of Accumulibacter, one of the members of the 18.2 Gb metagenome of the bacterial community attached to a EBPR plant, to its reference. The comparison reveals significant differences in gene content and metabolic potential.

Albertsen M, Hansen LB, Saunders AM et al. 2011 A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal The ISME journal

// circos-metagenome

Circos tackles the connectome

Irimia et al. introduce circular representation of cortical networks in Circular representation of human cortical networks for subject and population-level connectomic visualization. The scalability of this circular visualization approach is demonstrated by lucid aggregate visualizations using cortical networks of 50 individuals.

The UCLA group also used the circular connectome visualization to assess differences in brain injury in patients Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury in Frontiers in Neurotrauma.

A good layman description of the work can be found at the neurosceptic blog.

Irimia A, Chambers MC, Torgerson CM et al. 2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage

Irimia A, Chambers MC, Torgerson CM et al. 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3

// circos-cortical-network

From Degree to Job — Circos Visualizes Workforce Transitions

Finding the relationship between a student's major and career field is the topic of "Measuring Transitions Into The Workforce As A Form Of Accountability". The diagrams connect the flow of students from one of 17 fields of study (left) to job sectors (right).

Schenk TL, Jr. 2011 Measuring Transitions into the Workforce as a Form of Accountability SSRN eLibrary ID 1831967

// workforce

Circle of Cancer

This Circos depiction of a tumor genome provides the cover of 30 November 2011 Science's Transitional Medicine issue in which Roychowdhury et al. describe personalized treatment for patients with colorectal and prostate cancer. By quickly sequencing normal and tumor DNA and RNA, suitable therapies can be tailored for the specific mutations identified.

1Roychowdhury S, Iyer MK, Robinson DR et al. 2011 Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study Science Translational Medicine 3:111ra121.

// circleofcancer

Circos Helps Stomach Differences in Gut Bugs

Biggs et al. report on the evolution of Campylobacter jejuni ST-474, an important human enteric pathogen, through a comparison of two flaA SVR-14 isolates and other available C. jejuni isolates and genomes.

Biggs PJ, Fearnhead P, Hotter G et al. 2011 Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage PLoS One 6:e27121.

// campylobacter

Interactive Visualization of Structural Variation

Park et al. use the Circos paradigm to explore predicted structural variation. "Seqeyes is a novel multi-scale visualization that can interactively navigate dozens of genomes down to individual sequencing reads within a web browser."

Park R, Gehlenborg N, Park P. 2011. Seqeyes: A multi-scale interactive visualization tool for structural variations. In 1st IEEE Symposium on Biological Data Visualization, Providence, RI.

// seqeyes

Towards a Human Pan-Genome

As reported in Wired, Li et al. use Circos to visualize the comparison of structural variation in two sequenced human genomes: Asian and Yoruban (African). It's been over 10 years since the first reference genome (comprising DNA from multiple individuals) was reported. Technological advancements have made it possible to now sequence 1000's of human genomes to identify genetic variations for tracing evolution, determining population patterns, and assessing disease susceptibility and other phenotypic traits.

Li Y, Zheng H, Luo R et al. 2011 Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly Nature biotechnology 29:723-730.

Li R, Li Y, Zheng H et al. 2010 Building the sequence map of the human pan-genome Nature biotechnology 28:57-63.

// circos-denovovariation

Hemolytic–Uremic Syndrome Outbreak

Rasko et al. use Circos to show how the E. coli strain implicated in the German outbreak of hemolytic-uremic syndrome varies from other strains in their New England Journal of Medicine paper, where they find that "the genome of the German outbreak strain can be distinguished from those of other O104:H4 strains because it contains a prophage encoding Shiga toxin 2 and a distinct set of additional virulence and antibiotic-resistance factors."

NEJM created an animation that explains the visualizations. The paper was blogged by Pacific Biosciences.

Rasko DA, Webster DR, Sahl JW et al. 2011 Origins of the E. coli Strain Causing an Outbreak of Hemolytic-Uremic Syndrome in Germany The New England journal of medicine published ahead of print:-.

// nejm-hemoliticuremic

Circos in Simon Fraser University's AQ magazine (Apr 2011)

A Circos image appears as part of a spread in SFU's biannual AQ Magazine. The composite accompanies my photos of our laboratory and computer equipment.

The image was adapted from Figure 1 of our paper "Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors".

Jones SJ, Laskin J, Li YY et al. 2010 Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Genome Biol 11:R82.

// circos-aq

Linux kernel exploration

Răzvan Musăloiu-E. explored the Linux file system and used Circos to relate the systems (disk-based, optical mediums, flash-based, network-based, cluster-based, memory-based, ancient) to kernel symbols.

// linux-kernel-tux

Circos Helps with Urban Planning

The town of Caceres, Spain, a UNESCO World Heritage Site, used Circos to illustrate the relationships between businesses in their urban planning strategy.

// circos-caceres

Hive Plots - Linear Layout for Network Visualization

Visualizing large networks is hard. Nobody wants to see another hairball, but you want to show your data.

What do you do?

Try our new linear layout for network visualization, introducing the hive plot. This plot takes a fresh approach to drawing networks. It scales well, shows topology, and makes the network layout based on meaningful properties.

// linnet

Circos Collaborates with Wired

When Wired needed an inforgraphic to illustrate the complex world of relationships on the TV Series Lost, it turned to Circos.

In collaboration with Christy Sheppard, Wired's Art Director, Martin Krzywinski created the illustration for the April 22 2010 issue.

// wired-01