The terrifying dinosaur corn genome

Amblin Entertainment and Legendary Pictures, the studios that produced Jurrasic World, try to inject genome science into the movie. Unfortunately, since we don't quite know how to construct viable genomes of extinct species, much less grow the creatures themselves, we don't know whether the depiction of the science is right. Perhaps theirs is exactly what a genome lab would look like in a dino-building facility.

But, we can get fewer things wrong. In the Creation Lab companion website, a Circos image is used to illustrate a triceratops genome.

Unfortunately, this is an image of the B73 Maize reference genome (B73 RefGen_v1), as published in Nature's The B73 Maize Genome: Complexity, Diversity, and Dynamics.

Schnable PS Ware D Fulton RS et al. 2009 The B73 maize genome: complexity, diversity, and dynamics Science 326 (5956) 1112-1115

Using News Reports to Track Wildlife Black Markets

http://www.wired.com/2015/06/using-news-reports-track-wildlife-black-markets/

THE INTERNATIONAL BLACK market in wildlife—alive or dead—is notoriously difficult to track. Hunters and smugglers don’t report their take for the same reasons that drug dealers don’t report profits to the IRS. But if you could actually track those networks, maybe you could do something about them. That’s what sent Nikkita Patel, a veterinary epidemiologist at the University of Pennsylvania, to an unusual source of data on the illegal wildlife trade: the news.

—Wired

The image shows the illegal global rhinoceros trade network before (top) and after (bottom) a hypothetical targeted disruption. Created with Circos online table viewer.

Circos on Cancer Discovery Covers

The July 2013 issue cover shows a Circos plot of relative copy number changes in 38 oral squamous cell carcinoma tumors.

The September 2012 issue cover shows a collection of Circos images of somatic mutations in melanoma tumors.

July 2013 Pickering CR, Zhang J, Yoo SY et al. 2013 Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers Cancer discovery 3:770-781.

Sep 2012 Dahlman KB, Xia J, Hutchinson K et al. 2012 BRAF(L597) mutations in melanoma are associated with sensitivity to MEK inhibitors Cancer discovery 2:791-797.

Circos charts the placenta transcriptome

Saben et al. use Circos to visualize the transcriptome and gene expression of placenta from 20 healthy women in their article A comprehensive analysis of the human placenta transcriptome.

Saben J, Zhong Y, McKelvey S et al. 2014 A comprehensive analysis of the human placenta transcriptome Placenta 35:125-131.

Circos Maps America’s Restless Interstate Migration Without a Map

Wired has a writeup about migration patterns within the US that shows the data using d3.js chord diagrams, modeled after how Circos shows tabular data.

Circos on cover of UCSF Magazine

The Fall 2013 issue of UCSF Magazine has my Circos illustration of personalized medicine. The human outline motif is incorporated into other design elements in the issue.

The look of the image is inspired after Nature's Encode cover by Carl De Torres.

To learn how to generate the cover and variants, read the Circos Encode Cover Tutorial.

Circos on Cover of Cancer Cell

Yang et al. used network analysis approaches characterize a subtype of ovarian cancer associated with poor overall survival.

E-cadherin is a protein encoded by the CDH1 gene and is responsible for cell-cell adhesion. Yang linked the expression of E-cadherin to specific miRNAs that influenced the regulatory network singled out in this cancer subtype.

Yang D, Sun Y, Hu L et al. 2013 Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer Cancer cell 23:186-199

Circos reaches 500 literature citations

In October 2013 Circos reached a milestone - 500 citations in peer-reviewed literature.

To celebrate, I've made a commemorative poster that features over 400 Circos images from the literature.

citation list | image gallery | press highlights

Circos deals with 8 Gb Rye Genome

Because of its large 8 Gb genome, the genomic analysis of rye has lagged behind other cereals.

To address this, Martis et al. eastablished a linear gene order model for 72% of the rye genes based on synteny information from rice, sorghum and B. distachyon.

Although it appears that six major translocations shaped the modern rye genome, highly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks.

Martis MM, Zhou R, Haseneyer G et al. 2013 Reticulate Evolution of the Rye Genome Plant Cell

Circos Stages Mesolithic to Neolithic Transition

Bollongino et al. present evidence of a slow transition between Mesolithic hunter-gatherer groups to Neolithic farmers.

Previous theories that the foragers disappeared shortly after the arrival of farmers are at odds with palaeogenetic and isotopic data analysis from Neolithic human skeletons from the Blätterhöhle burial site in Germany. Instead of an abrupt transition, the data suggest a more complex pattern of coexistence that persisted for over 2000 years.

Bollongino R, Nehlich O, Richards MP et al. 2013 2000 years of parallel societies in Stone Age Central Europe Science 342:479-481.

Circos in 54 million pixels

Ruddle et al. demonstrate their commodity hardware 54 million pixel data display in exploring copy number variation data.

Ruddle RA, Fateen W, Treanor Det al.. 2013. Leveraging Wall-sized High-Resolution Displays for Comparative Genomics Analyses of Copy Number Variation. In IEEE Symposium on Biological Data Visualization, Atlanta, GA.

Circos Tracks CO₂ Emissions

Kanemoto et al. report on the disturbing trend of emissions leakage, in which developing countries are displacing emissions intensive production offshore.

The report confirms previous findings that adjusting for trade, developed countries emissions have increased, not decreased. A connection is made to the kind of emissions displacement that has already occurred for air pollution, where despite aggressive legislation in major emitters total global air pollution emissions have increased.

The conclusion warns us that "if regulatory policies do not account for embodied imports, global emissions are likely to rise even if developed countries emitters enforce strong national emissions targets."

Kanemoto K, Moran D, Lenzen M et al. 2013 International trade undermines national emission reduction targets: New evidence from air pollution Global Environmental Change

Circos Round — Lotus Sacred

The pleasing roundness of Circos is used by Ming et al. to depict the Sacred Lotus genome in the publication "Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).

The Sacred lotus has religious significance in both Buddhism and Hinduism and has been used as a food and herbal medicine product in Asia for over 7,000 years. Its seeds have exceptional longevity, remaining viable for as long as 1,300 years.

The plant is known for its exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.

Ming R, Vanburen R, Liu Y et al. 2013 Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Genome Biol 14:R41.

6.9e11 g of oil and Circos was there

Rivers et a. describe the effects of the Deepwater Horizon blowout on the microbial blooms of petroleum-degrading bacteria.

By sequencing 66 million community transcripts, the identity of metabolically active microbes and their roles in petroleum consumption was revealed.

Rivers AR, Sharma S, Tringe SG et al. 2013 Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill The ISME journal

Plants Love Circos

Circos frequently appears in plant literature, twice on the cover of Plant Biotechnology Journal in the last year.

Rai KM, Singh SK, Bhardwaj A et al. 2013 Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes Plant biotechnology journal

Bekele WA, Wieckhorst S, Friedt W et al. 2013 High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array Plant biotechnology journal

Circos has appeared 8 times each in the Plant Journal and Plant Cell.

Circos for R

Zhang et al. implement Circos in R.

Same round shape you expect. And now, in everyone's favourite open source statistics and data analysis environment.

CRAN RCircos package

Zhang H, Meltzer P, Davis S 2013 RCircos: an R package for Circos 2D track plots BMC Bioinformatics 14:244.

Circos Interchange Diagrams — Networks and Flow

Zeng et al. introduce a new type of visualization based on Circos, the interchange diagram, in their paper Visualizing Interchange Patterns in Massive Movement Data.

The design is applied to displaying movement data, such as daily trips made by passengers in a city. By incorporating interactivity, this visualization method is helpful to understand interchange patterns at different spatial (between trains, between cities) and time scales (different times of day).

Circos has been used for urban planning before. The town of Caceres in Spain has used Circos to communicate their urban planning strategy.

project website

Zeng W, Fu C-W, Arisona SM et al. 2013 Visualizing Interchange Patterns in Massive Movement Data Computer Graphics Forum 32:271-280

Circos connects to the connectome

Methods to visualize the connectome are reviewed in Craddock et al — Circos is one of them.

Craddock RC, Jbabdi S, Yan C-G et al. 2013 Imaging human connectomes at the macroscale Nat Meth 10:524-539.

The use of Circos for showing the connectome was introduced by Irimia et al. in Circular representation of human cortical networks for subject and population-level connectomic visualization.

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 is the Method for Visualizing Translocations

Genomic rearrangements can cause disease and are implicated in many cancers. Being able to see the patterns in these changes across samples and patients is important.

In the review article End-joining, Translocations and Cancer, Bunting and Nussenzweig demonstrate how compositing the genome circularly adds value and clarity to the presentation.

Bunting SF, Nussenzweig A 2013 End-joining, translocations and cancer Nat Rev Cancer

Circos Paints Chromosomes of Capsella Rubella

Slotte et al. use Circos to show the genomic structures, chromosome painting and comparative genomic mapping in C. rubella, A. lyrata and A. thaliana.

Their figure illustrates how Circos is effective at showing two-way comparisons of syntenic structure. For three-way comparison, consider hive plots.

Slotte T, Hazzouri KM, Agren JA et al. 2013 The Capsella rubella genome and the genomic consequences of rapid mating system evolution Nat Genet

Circos on the Cover Of Journal of Pathology

The June 2013 issue of the Journal of Pathology features a pair of Circos plots on the cover. The images are from the paper by Weier et al. describing TMPRSS2 and ERG rearrangements in prostate cancer.

"TMPRSS2–ERG rearrangements occur in approximately 50% of prostate cancers and therefore represent one of the most frequently observed structural rearrangements in all cancers."

Weier C, Haffner MC, Mosbruger T et al. 2013 Nucleotide resolution analysis of TMPRSS2 and ERG rearrangements in prostate cancer J Pathol 230:174-183.

Circos on the Cover Of Nature's Asian Journal of Andrology

The May 2013 Special Issue of Asian Journal of Andrology presents the outcomes from the Sixth Annual Forum on Prostate Disease (6th FPD), which was held on June 8-9, 2012 in Shanghai, China [source: nature.com]. The cover art for the issue shows a Circos plot of 90 significantly recurrent molecular alterations in prostate cancer from an analysis of 372 prostate tumors discussed in the Wyatt et al. review article.

The review summarizes the current state of understanding of prostate cancer, "including the sentinel role of copy number variation, the growing spectrum of oncogenic fusion genes, the potential influence of chromothripsis, and breakthroughs in defining mutation-associated subtypes. Increasing evidence suggests that genomic lesions frequently converge on specific cellular functions and signalling pathways, yet recurrent gene aberration appears rare".

Wyatt AW, Mo F, Wang Y et al. 2013 The diverse heterogeneity of molecular alterations in prostate cancer identified through next-generation sequencing Asian J Androl 15:301-308.