SANTA - Spatial Analysis of NeTwork Associations

A festive bioinformatics acronym today: SANTA - Spatial Analysis of NeTwork Associations. The authors don't make a big deal of the acronym in the paper but it seemed contrived enough for a Christmas ORCA entry.

Abstract

Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology. Here, we adapt concepts of spatial statistics to assess the functional content of molecular networks. Based on the guilt-by-association principle, our approach (called SANTA) quantifies the strength of association between a gene set and a network, and functionally annotates molecular networks like other enrichment methods annotate lists of genes. As a general association measure, SANTA can (i) functionally annotate experimentally derived networks using a collection of curated gene sets and (ii) annotate experimentally derived gene sets using a collection of curated networks, as well as (iii) prioritize genes for follow-up analyses. We exemplify the efficacy of SANTA in several case studies using the S. cerevisiae genetic interaction network and genome-wide RNAi screens in cancer cell lines. Our theory, simulations, and applications show that SANTA provides a principled statistical way to quantify the association between molecular networks and cellular functions and phenotypes. SANTA is available from http://bioconductor.org/packages/release​/bioc/html/SANTA.html.

Ref: Cornish AJ & Markowetz F (2014) SANTA: Quantifying the Functional Content of Molecular Networks. PLoS Comput Biol 10(9): e1003808.

REACH - Registration, Evaluation, Authorisation and Restriction of Chemicals

REACH - Registration, Evaluation, Authorisation and Restriction of Chemicals is a fine example of acronym contrivance (although lacking the panache of a good pre hoc concoction). Not got the right words for something catchy? Just ignore the inconvenient word!

“[REACH] streamlines and improves the former legislative framework on chemicals of the European Union (EU). The main aims of REACH are to ensure a high level of protection of human health and the environment from the risks that can be posed by chemicals, the promotion of alternative test methods, the free circulation of substances on the internal market and enhancing competitiveness and innovation.”

I guess you can’t blame them for trying to make it more interesting.

MUSIC - MUltiScale enrIchment Calling

Over on the ACGT blog, Keith Bradnam has another JABBA Award (and a nice new JABBA logo):

MUSIC - Multiscale Enrichment Calling.

I'm not sure what the connection between MUSIC and ChIP-Seq is but the authors seemed pretty determined. His post is actually a twofer, as it also draws attention to an equally contrived an unfathomable intranym:

MuSiC - Multiple Sequence Alignment with Constraints

Read more at Keith’s blog!

DREAM - Dialogue for Reverse Engineering Assessments and Methods

According to the website, DREAM is a Dialogue for Reverse Engineering Assessments and Methods:

“The main objective is to catalyze the interaction between experiment and theory in the area of cellular network inference and quantitative model building in systems biology.”

Not clear?

“DREAM (Dialogue for Reverse Engineering Assessments and Methods) poses fundamental questions about systems biology, and invites participants to propose solutions. The main objective is to catalyze the interaction between theory and experiment, specifically in the area of cellular network inference and quantitative model building. DREAM challenges address how we can assess the quality of our descriptions of networks that underlie biological systems, and of our predictions of the outcomes of novel experiments. These are not simple questions. Researchers have used a variety of algorithms to deduce the structure of biological networks and/or to predict the outcome of perturbations to their systems. They have also evaluated the success of their methodologies using a diverse set of non-standardised metrics. What is still needed, and what DREAM aims to achieve, is a fair comparison of the strengths and weaknesses of these methods and a clear sense of the reliability of the models that researchers create.”

I know a bit about Systems Biology but I must admit to being confused about the “Assessment and Methods” part of DREAM. I think it means that DREAM is about assessing methods and models for reverse engineering biological systems (i.e. Systems Biology), even though it reads that they are trying to reverse engineer assessments and methods. Such dedication to the acronym over clarity makes DREAM a worthy ORCA entry.

ILIaD - Institute for Learning Innovation and Development

The learning and teaching unit at the University of Southampton has had a few different names over the years but its latest incarnation is ORCA-worthy with some selective use of prepositions: ILIaD - the Institute for Learning Innovation and Development. Find out more at the ILIaD website. (Although ILIaD is undoubtedly replete with heroes, I think this is ad hoc.)

MAGIC - the Meta-Analyses of Glucose and Insulin-related traits Consortium

The final human genetics consortium (for now) is MAGIC - the Meta-Analyses of Glucose and Insulin-related traits Consortium, another co-author of the DIAGRAM consortium. This is probably the most contrived of the lot, in that it failed to use all its words but did include “Consortium”. At the same time, being part of MAGIC has a certain appeal above CHARGE, DIAGRAM or GIANT.

“MAGIC (the Meta-Analyses of Glucose and Insulin-related traits Consortium) represents a collaborative effort to combine data from multiple GWAS to identify additional loci that impact on glycemic and metabolic traits.

MAGIC investigators have initially studied fasting glucose, fasting insulin, 2h glucose and HBA1c, as well as performed meta-analysis of more sophisticated measures of insulin secretion and sensitivity. Through these efforts, dozens of loci influencing these traits have been idenified, a subset of which also influence risk of type 2 diabetes.”

There is a certain degree of magic involved in a good genome-wide association study (GWAS) but I still rate this one ad hoc.

If contrived consortium acronyms are your thing, you can probably do a lot worse than sign up to the Table of Contents alerts for the journal Nature Genetics.

GIANT - Genetic Investigation of ANthropometric Traits

Human genetics consortium number three is the GIANT - Genetic Investigation of ANthropometric Traits - consortium, a co-author of one of the recent DIAGRAM papers in Nature Genetics.

“The Genetic Investigation of ANthropometric Traits (GIANT) consortium is an international collaboration that seeks to identify genetic loci that modulate human body size and shape, including height and measures of obesity. The GIANT consortium is a collaboration between investigators from many different groups, institutions, countries, and studies, and the results represent their combined efforts. The primary approach has been meta-analysis of genome-wide association data and other large-scale genetic data sets. Anthropometric traits that have been studied by GIANT include body mass index (BMI), height, and traits related to waist circumference (such as waist-hip ratio adjusted for BMI, or WHRadjBMI). Thus far, the GIANT consortium has identified common genetic variants at hundreds of loci that are associated with anthropometric traits.”

Genome-wide association studies are big by nature, and GIANT does have a lot of participating cohorts and groups on their webpage, so I think that GIANT can be given a post hoc rating.

DIAGRAM - DIAbetes Genetics Replication And Meta-analysis

The DIAGRAM - DIAbetes Genetics Replication And Meta-analysis - consortium is the second ORCA entry this month for human genetics consortia, which seem to be almost as productive a source of contrived acronyms as bioinformatics.

“The DIAGRAM (DIAbetes Genetics Replication And Meta-analysis) consortium is a grouping of researchers with shared interests in performing large-scale studies to characterise the genetic basis of type 2 diabetes, and a principal focus on samples of European descent.”

You can read more on their website, which features an array of additional acronyms (including some future ORCA entries).

CHARGE - Cohorts for Heart and Aging Research in Genomic Epidemiology

The CHARGE - Cohorts for Heart and Aging Research in Genomic Epidemiology - consortium is the first of four human genetics consortia to hit ORCA this month.

I’m not really sure what tigers have to do with hearts or aging, or even charging for that matter, but it’s a nice logo. Coordinating research with that many participants must be challenging enough - I am not sure how you contrive an acronym and logo that everyone agrees with!

According to the CHARGE consortium website:

"The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium was formed to facilitate genome-wide association study meta-analyses and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies."

• Psaty BM, O’Donnell CJ, Gudnason V, Lunetta KL, Folsom AR, Rotter JI, Uitterlinden AG, Harris TB, Witteman JCM, Boerwinkle E, on behalf of the CHARGE Consortium (2009) Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium: Design of prospective meta-analyses of genome-wide association studies from five cohorts. Circ Cardiovasc Genet. 2:73-80.

PEPPER - Protein complex Expansion using Protein-Protein intERactions

Another offering from the ever-fruitful world of bioinformatics today - with a fruit, fittingly enough.

PEPPER - Protein complex Expansion using Protein-Protein intERactions - pulls out all the stops when it comes to contriving a functional word, skipping words and using internal letters.

For the curious, PEPPER is available from the Cytoscape App Store and is:

“designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the coverage, a solution must contain as many proteins from the seed as possible, (ii) the density, the proteins of a solution must be as connected as possible, using only interactions from a proteome-wide interaction network.”

Despite its use of “seed lists”, I don’t think there is a direct connection with peppers, so PEPPER is being classified as an ad hoc intranym.

I’m not sure if there’s a bigger version of the logo available but if you look carefully, you can see the little chilli peppers.

Winterhalter C et al. (2014) PEPPER: cytoscape app for protein complex expansion using protein-protein interaction networks. Bioinformatics. Aug 18. pii: btu517. [Epub ahead of print]

WImpiBLAST - Web Interface for mpiBLAST

Although BLAST is a deserved ORCAcronym in its own right, it is also notable for the number of spin-offs and add-ons that it has produced. One such program is mpiBLAST, an open-source parallelisation of BLAST. This is turn has spawned WImpiBLAST - Web Interface for mpiBLAST. I’m not sure if WImpiBLAST deserves a new “anti hoc” class of acronym, as parallelisation of BLAST on a supercomputer is anything but wimpy. Ad hoc will do for now.

You can find out more at RNA-Seq Blog or the paper:

• Sharma P & Mantri SS (2014) “WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing.” PLoS ONE 9(6): e101144.

BLAST - Basic Local Alignment Search Tool

If there is one bioinformatics program that every biologist has heard of, it is BLAST: Basic Local Alignment Search Tool. In fact, BLAST is so popular and famous that many people probably don’t know that it is an acronym nor what it stands for; “to BLAST” has become a verb in common use. For non-biologists, BLAST is a homology search tool, which means that it finds similarities between biological (nucleotide or protein) sequences, and biologists will frequently “BLAST a sequence against a database” to find similar sequences.

The original BLAST algorithm is pretty old, which is part of the reason for its widespread fame. I’m not sure of the stats but the original Altschul et al. (1990) paper must be one of the most cited of all time.

• Altschul S, Gish W, Miller W, Myers E & Lipman D (1990). “Basic local alignment search tool”. Journal of Molecular Biology 215 (3): 403–410.

Certainly a worth addition to ORCA. (Although the main motivation for adding it is for the next post!) Given that BLAST works by fragmenting the query sequence into pieces for the initial search, I think that it rates at least as a post hoc.

MFSPSSMpred - Masked, Filtered and Smoothed Position-Specific Scoring Matrix-based predictor

Today’s post is a bit odd, as it is an anti-ORCA acronym. There is a reason why contrived acronyms exist, and I think that MFSPSSMpred is a prime example. The acronym itself is almost informative, although it fails to identify what it is trying to predict. (Short molecular recognition features in this case.) Still, imagine yourself in a lab meeting, trying to tell your supervisor which prediction tool you were using from memory!

MFSPSSMpred does have one thing going for it, though, and that’s Google-friendliness. Providing you spell it right, that is!

P.S. Whilst Googling MFSPSSMpred, I discovered that OCTAGON-winning Keith Bradnam got there first and MFSPSSMpred is a JABBA Award winner!

ARENA - Australian Renewable ENergy Agency

ARENA is the Australian Renewable Energy Agency,

an independent agency established by the Australian Government on 1 July 2012. We have two objectives: to improve the competitiveness of renewable energy technologies, and to increase the supply of renewable energy in Australia.

Unfortunately, ARENA was one of the losers from the recent Australian budget and might not be around much longer.

HOTAIR - HOX Transcript Antisense RNA

According to Wikipedia:

HOTAIR (for HOX antisense intergenic RNA) is a human gene located on chromosome 12. It is the first example of an RNA expressed on one chromosome that has been found to influence transcription on another chromosome.

However, Wikipedia itself cites Genecards, which has a slightly different metanym expansion (without any missing letters) for HOTAIR: HOX Transcript Antisense RNA. Either way, a very interesting gene and, though ad hoc intranym, certainly contrived enough for ORCA!

(HOTAIR possibly needs a new ORCA classification because both “metanym” sub-acronyms - HOX (Homeobox) and RNA (Ribonucleic acid) are themselves “itranyms”, as is HOTAIR.)

MODULUS - Methods Of Determining and Understanding Light elements from Unequivocal Stable isotope compositions

Another one from Rosetta, MODULUS - Methods Of Determining and Understanding Light elements from Unequivocal Stable isotope compositions - is described in Cosmos as part of the PTOLEMY instrumentation "to understand the geochemistry of light elements, such as hydrogen, carbon, nitrogen and oxygen".

That’s a lot of words and definitely an ORCA level of commitment to contrive a word out of it, even if they were not able to use them all!

miRCat - miRNA Categoriser

I am currently writing some lectures on RNA biology and came across the charmingly named miRCat: miRNA Categoriser.

This is a meta-acronym, with miRNA being short for microRNA (often abbreviated further to "miR" and pronounced “meer”, hence the logo) and RNA itself an acronym for Ribonucleic Acid).

miRCat is a tool to identify miRNAs in high-throughput small RNA sequence data… miRCat takes a FASTA file of small RNA reads as input and will map them to a reference genome… The tool then looks at genomic hit distribution patterns and secondary structure of genomic regions corresponding to sRNA hits and will predict miRNAs and their precursor structures.

Given the homophonic aspect of the acronym, I reckon this counts as pre hoc. As far as I am aware, “Categoriser” is not even a real (English) word, so this is definitely acronym contrivance worth of ORCA.

New ORCA acronym listings page

Just for a bit of extra organisation, there is now an alphabetical listing of acronyms featured in ORCA.

TARDIS - TARDigrades In Space

Yesterday’s TARDIS post was preamble for another TARDIS: Tardigrades in Space. This TARDIS is science rather than science fiction and you can read about it at the Tardigrades In Space blog.

Tardigrades In Space or “TARDIS” is the first research project to evaluate the ability of tardigrades to survive under open space conditions. TARDIS is one of the projects within the Biopan-6 research platform provided by European Space Agency (ESA), and will be sent into space with the russian FOTON-M3 mission.

Apparently, Tardigrades (a.k.a. “waterbears” or "moss piglets") can survive the vacuum and cosmic radiation of space.

h/t: This one is a submission from reader vardis.

TARDIS - Time And Relative Dimension In Space

Like many geeks, I am a fan of the rebooted Dr Who science fiction series.

As I suspect everyone with internet access knows, the Doctor’s spaceship-come-time-machine is the (or a) TARDIS: Time And Relative Dimension In Space.

It’s not my favourite acronym, I must admit, but it certainly is contrived. It is also a good excuse to share the photo on the left of the TARDIS in beautiful knitted form from the recent Royal Easter Show in Sydney. (Bravo, Andrew Galagher!) Mostly, though, it is a primer for the next ORCA post.

(NB. I always thought that the “Dimension” was plural but apparently not. I don’t really think that it makes sense in the singular but what do I know?)

SESAME - Surface Electric Sounding and Acoustic Monitoring Experiment

As well as providing several years of geeky suspense from its launch in 2004 until its comet landing later this year, the Rosetta mission is replete with acronyms. One of the most ORCA-worthy of these is SESAME, the Surface Electric Sounding and Acoustic Monitoring Experiments.

Three instruments measure properties of the comet’s outer layers. The Cometary Acoustic Sounding Surface Experiment (CASSE) measures the way in which sound travels through the surface. The Permittivity Probe (PP) investigates its electrical characteristics, and the Dust Impact Monitor (DIM) measures dust falling back to the surface.

Not a space-related word but still a good ad hoc algorithm.

TrIPE - T. rex International Paleontonomics Experiment (TrIPE)

The T. rex International Paleontonomics Experiment (TrIPE) was responsible for the Tyrannosaurus rex draft genome, released on 1st April 2003 and described as “the genetic blueprint for the most important of the dinosaurs used in genetics today”. Unfortunately, it is no longer available on the Ensembl genome database, having been withdrawn for being totally fabricated. ☺

[Image from Wikimedia Commons]

CRAPome - Contaminant Repository for Affinity Purification

Purists might argue that the “ome” stops this being a true acronym but, for me, there can be few finer examples of the art of the contrived acronym than CRAPome - Contaminant Repository for Affinity Purification [for mass spectrometry proeome data]:

Mellacheruvu D et al. (2013). “The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.” Nat Methods 10(8): 730-736.

Affinity purification coupled with mass spectrometry (AP-MS) is a widely used approach for the identification of protein-protein interactions. However, for any given protein of interest, determining which of the identified polypeptides represent bona fide interactors versus those that are background contaminants (for example, proteins that interact with the solid-phase support, affinity reagent or epitope tag) is a challenging task. The standard approach is to identify nonspecific interactions using one or more negative-control purifications, but many small-scale AP-MS studies do not capture a complete, accurate background protein set when available controls are limited. Fortunately, negative controls are largely bait independent. Hence, aggregating negative controls from multiple AP-MS studies can increase coverage and improve the characterization of background associated with a given experimental protocol. Here we present the contaminant repository for affinity purification (the CRAPome) and describe its use for scoring protein-protein interactions. The repository (currently available for Homo sapiens and Saccharomyces cerevisiae) and computational tools are freely accessible at http://www.crapome.org/.

Pre hoc genius!

SPICE - Stratospheric Particle Injection for Climate Engineering

Climate Change is upon us, whether we like/admit it or not. Whilst some are still hopeful that we can halt and reverse the trend in emissions that has us seeing CO₂ and global temperatures outside the range of all human history, others are beginning to devise and test Plan B: Geoengineering (or “Climate Engineering”) our way out of trouble.

One such project is SPICE - Stratospheric Particle Injection for Climate Engineering.

The SPICE project is investigating the effectiveness of Solar Radiation Management (SRM). SRM involves offsetting the effects of greenhouse gas increases by causing the Earth to absorb less radiation from the Sun.

It should be noted that SPICE are not actually planning/promoting injecting stuff into the atmosphere - it could potentially be really bad news - but instead are “investigating the feasibility, risks and governance associated with Solar Radiation Management”. By the time that things get so bad that we need this sort of stuff - a regrettably probable future in my opinion - it will be too late to start looking into it. (That said, there is a danger that by developing the technology, we make the application more likely. It’s a tricky one!)

SPICE is not too contrived as ORCA acronyms go but then it is not too relevant to climate change/engineering either.

h/t: BBC Discovery.

USA PATRIOT - Uniting and Strengthening America by Providing Appropriate Tools Required to Intercept and Obstruct Terrorism

No list of contrived acronyms could be complete without USA PATRIOT - Uniting and Strengthening America by Providing Appropriate Tools Required to Intercept and Obstruct Terrorism.

Another acronym featured on Wikipedia’s backronym page, the USA PATRIOT Act of 2001 is an oldie but goldie that has long been on ORCA’s radar. (As it happens, Radar is also an acronym - RAdio Detection And Ranging - and was originally RADAR but has become an everyday word, much like LASER - Light Amplification by the Stimulated Emission of Radiation.)

The USA PATRIOT Act is famous enough to need no introduction but so contrived that it had to feature at some point. Although listed as a “backronym” by Wikipedia, under ORCA classification it is definitely a pre hoc: something contrived to fit an appropriate word. Whether its an appropriate Act is a whole other issue.

CICADA - Cochlear Implant Club and ADvisory Association

The cicadas in Sydney are loud this year. Fitting, then, that CICADA is the chosen acronym for the Cochlear Implant Club and Advisory Association.

CICADA Australia Inc. began in 1984 as a support organization in NSW to help new cochlear implantees. At the time there were only 12 implantees. Implant surgeon Prof. Bill Gibson came up with the name intending that it should stand for “Cochlear Implant Club and Deafness Association”. However none of the newly implanted people felt they were still deaf, so a compromise was reached. The title later came to stand for “Cochlear Implant Club and ADvisory Association”.

As cochlear implants make things louder (in a very crude sense) and cicadas are among the noisiest insects in the world, I think there is a definite case to be made for a post hoc connection.

BRAIN - Brain Research through Advancing Innovative Neurotechnologies

On Friday, I had a little rant on The Cabbages of Doom that Climate Change was more worthy than brains for special funding attention. One of the brain projects that got said special funding last year (to the tune of $100m) was The BRAIN Initiative , which turns out to be a pre hoc acronym worthy of ORCA: Brain Research through Advancing Innovative Neurotechnologies. Vague technobabble at its finest!

Although the B of BRAIN itself stands for Brain, I don’t think that it count as recursive but it’s close.

CLARITY - Clear, Lipid-exchanged, Anatomically Rigid, Imaging/immunostaining compatible, Tissue hYdrogel

Another one that popped up in a journal Table of Contents (this time Science), CLARITY is the spectacularly contrived Clear, Lipid-exchanged, Anatomically Rigid, Imaging/immunostaining compatible, Tissue hYdrogel. As an acronym, it falls down at the end, so this one is being classed as an “intranym” but as CLARITY is a brain-imaging technique, I think it deserves pre hoc status. CLARITY was runner-up for Science journal’s Breakthrough of the Year.

SQUID - Superconducting QUantum Interference Device

SQUID - Superconducting QUantum Interference Device - came to my attention from a recent Nature magazine TOC featuring a News & Views piece, Quantum physics: An atomic SQUID:

“When a magnetic field needs to be measured with the utmost precision, a superconducting quantum interference device (SQUID) is the instrument of choice.”

I’m not aware that cephalopods are particularly good at quantum physics nor precise measurements of magnetic fields, so this one is rated ad hoc.