Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/035295

Interactive Analytics for Very Large Scale Genomic Data

Cuiping Pan·Nicole Deflaux·Gregory McInnes·Michael Snyder·Jonathan Bingham·Somalee Datta·Philip Tsao
View original source ↗Export metadata ↓

Abstract

Large scale genomic sequencing is now widely used to decipher questions in diverse realms such as biological function, human diseases, evolution, ecosystems, and agriculture. With the quantity and diversity these data harbor, a robust and scalable data handling and analysis solution is desired. Here we present interactive analytics using public cloud infrastructure and distributed computing database Dremel and developed according to the standards of Global Alliance for Genomics and Health, to perform information compression, comprehensive quality controls, and biological information retrieval in large volumes of genomic data. We demonstrate that such computing paradigms can provide orders of magnitude faster turnaround for common analyses, transforming long-running batch jobs submitted via a Linux shell into questions that can be asked from a web browser in seconds.

Source connections

Explore related subjects

Preprint

Keep this discovery

BibTeXRIS

Cuiping Pan, Nicole Deflaux, Gregory McInnes, Michael Snyder, Jonathan Bingham, Somalee Datta, Philip Tsao. 2015-12-24. Interactive Analytics for Very Large Scale Genomic Data. https://doi.org/10.1101/035295

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2017

Love, not food, could have paved the path for dog domestication: A lesson from free-ranging dogs

Dogs (Canis lupus familiaris) are the first species to have been domesticated, and unlike other domesticated species, they have developed a special bonding with their owners. The ability to respond to human gestures and language is a key factor in the socio-cognitive abilities of dogs that have made them our best friend. Free-ranging dogs provide an excellent model system for understanding the dog domestication process. In India, free-ranging dogs occupy every possible human habitation, and interact with humans regularly. They scavenge among garbage, beg for food from humans, give birth in dens close to human habitations, and establish social bonds with people. However, there is ample dog-human conflict on the streets, leading to morbidity and mortality. Hence the ability to assess an unfamiliar human before establishing physical contact could be adaptive for dogs especially in the urban environment. We tested a total of 103 adult free-ranging dogs to investigate their response to immediate and long-term food and social rewards. The dogs were provided a choice of obtaining a food reward either from the hand or the ground. The dogs avoided making physical contact with the unfamiliar human. While immediate rewards were not effective in changing this response, the long-term test showed a strong effect of the social reward on the response of dogs. Our results revealed that dogs tend to build trust based on affection, and not food rewards. This study provides significant insights into nuances of the dynamics that could have paved the path to dog domestication.

Preprint↗
bioRxiv2016

Chiral vortex dynamics on membranes is an intrinsic property of FtsZ, driven by GTP hydrolysis

The primary protein of the bacterial Z ring guiding cell division, FtsZ, has recently been shown to engage in intriguing self-organization together with one of its natural membrane anchors, FtsA. When co-reconstituted on flat supported membranes, these proteins assemble into dynamic chiral vortices whose diameters resemble the cell circumference. These dynamics are due to treadmilling polar FtsZ filaments, supposedly destabilized by the co-polymerizing membrane adaptor FtsA, thus catalysing their turnover. Here we show that FtsA is in fact dispensable and that the phenomenon is an intrinsic property of FtsZ alone when supplemented with a membrane anchor. The emergence of these chiral dynamic patterns is critically dependent on GTP concentration and FtsZ surface densities, in agreement with theoretical predictions. The interplay of membrane tethering, GTP binding, and hydrolysis promotes both, the assembly and the destabilization of FtsZ polymers, leading to the observed treadmilling dynamics. Notably, the vortex chirality is defined by the position of the membrane targeting sequence (mts) and can be inverted when attaching it to the opposite end of FtsZ. This reveals a so far unknown vectorial character of these cytomotive filaments, comprising three orthogonal directions: Filament polarity, curvature, and membrane attachment.

Preprint↗
bioRxiv2016

Global changes in patterning, splicing and primate specific lncRNAs in autism brain

We apply transcriptome-wide RNA sequencing in postmortem autism spectrum disorder (ASD) brain and controls and identify convergent alterations in the noncoding transcriptome, including primate specific lncRNA, and transcript splicing in ASD cerebral cortex, but not cerebellum. We characterize an attenuation of patterning between frontal and temporal cortex in ASD and identify SOX5, a transcription factor involved in cortical neuron fate specification, as a likely driver of this pattern. We further show that a genetically defined subtype of ASD, Duplication 15q Syndrome, shares the core transcriptomic signature of idiopathic ASD, indicating that observed molecular convergence in autism brain is the likely consequence of manifold genetic alterations. Using co-expression network analysis, we show that diverse forms of genetic risk for ASD affect convergent, independently replicated, biological pathways and provide an unprecedented resource for understanding the molecular alterations associated with ASD in humans.

Preprint↗