metabolic pathways: microarray analysis tools

Three generation approaches are today available for functional pathway analysis.

Just brief notes and many links for my (and perhaps your) memory and benefit. Based largely on this Plos Computational Biology review by Khatri et al., 2012.

Pathway-centric approaches are intended to reduce the complexity of the transcriptome profiling data and are well accepted because a significant modulation of a pathway (rather than single genes) is deemed to increase the explanatory power of the observations. 


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1st generation ORA: Over-Representation Analysis statistically evaluate the fraction of genes in a particular pathway found among the list of genes with significantly different fold changes. This is the most common analysis. Limitations: once the scientist select the list of genes, ORA treats each gene equally, irrespectful of fold changes. Thus, you miss marginally less significant genes causing some information loss that could be important inside a pathway. In addition, ORA approaches assume that for each gene, the FC is independent on other FC genes, which is not the case, for instance a decrease in one transcription factor can cause a decrease of its target genes.

2nd generation FCS: Functional Class Scoring. In response to ORA limitations, FCS methods assess ALL gene expression measurements, so they do not require an arbitrary threshold. Good to see effects on genes changing less than 2-fold. The most popular FCS approach is the Gene Set Enrichment Analysis (GSEA). GSEA ranks all the gene expression changes and map their significant over-representation inside a pathway (called gene set). One possible limitation is that the fold changes are used only to make the rank. The rank than is used for statistical analysis. Other people say this is good because gives robustness to outliers.

3rd generation PT: Pathway Topology-based approaches. Both ORA and FC methods consider a pathway just like a gene set: nothing more than a list of genes. However, inside a pathway, the genes have diffeent relationships. The pathway topology describes the shape of these logical relationships and defines the features of the corresponding network between the genes in the pathway. Instead of considering the most different genes (ORA) or the whole rank of gene expression (FC), the third generation algorithms use topological informations to compute the statistics, similarly to what the Google PageRank makes with internet pages. The major limitation is the fact that most topological relationships are poorly curated in biological knowledge-bases, and some relationships are reportedly tissue-specific, so few PT-based tools are available as complete stand-alone solutions.

Note: don't be fooled by the title, other than microarrays, these approaches are valid for other mRNA profiling technologies including nanostring and RNA-seq. In addition, the same pathway-centric statistics can be applied to 'omics' profiling experiments other than RNA.

Solve puzzles for science


In science, game-driven crowdsourcing makes 18 fold better

Because of sequential nature of mRNA translation, proteins begin as strings of 50-1000 amino acids that immediately fold into specific 3D-coiled structures. Understanding how proteins fold into unique three-dimensional shapes is a big quest. Just a small protein can fold in astronomical number of ways, so one of the hardest problems in biology today is to figure out, for each protein, which of the many possible structures is the most correct one. Scientists try to solve this jigsaw puzzle because it may help to understand how a protein carries out its job.

Computers make faster permutations, and different automatic algorithms try to estimate protein folding. Sometimes however, human creativity can outperform the computer processivity, so in 2008 a team of HHMI researchers at the University of Washington decided to take the arcane world of protein folding to the online gaming arena. Foldit is a free game in which players around the world compete to design proteins. Foldit attempts to predict the structure of a protein by taking advantage of humans puzzle-solving intuitions and having people play competitively to fold the best proteins.


Four years later, Nature Biotechnology is publishing today a study of the original team where Foldit players were challenged to ameliorate the structure of a Dies-Alderase enzyme, a protein holding great promises for the production of renewable fuels.
Here we report the use of game-driven crowdsourcing to enhance the activity of a computationally designed enzyme through the functional remodeling of its structure [...] Several iterations of design [...] increased enzyme activity >18-fold. X-ray crystallography showed that the large insertion adopts a helix-turn-helix structure positioned as in the Foldit model. These results demonstrate that human creativity can extend beyond the macroscopic challenges encountered in everyday life to molecular-scale design problems.


---/ Original source / --- ---
Eiben et al., Nature Biotechnology 30, 190 (2012). doi:10.1038/nbt.2109 

DIY Research: how to start their own

It is possible for researchers to start their own private lab?
If in your life you want to sell pizza, it is easy to find a business plan: just open a pizza shop. But if you want to sell science, and you want to do it by yourself, in your garage rather than corporate in some academy or industry... Is it possible? Remember this name: InnoCentive. It will work also if you have already a job but have some spare-time to develop additional rewarding projects on the side. Sometimes, no more than a written proposal is required, and even if you don't have pipettes and centrifuges at home, you can just sell your ideas.

Got an idea? Sell it. Picture by Wonderferret

InnoCentive: a rewarding solution to DIY science projects.
InnoCentive believes that great solutions to tough problems can come from anywhere. Seeker organizations work with InnoCentive team to formulate and host Challenges with awards ranging from $5,000 to $1 million. They've already awarded over $9 million and counting - with some hard work and ingenuity, you could be the next winning Solver! In this post, I will introduce you to how InnoCentive works, and what you can do to become a successful and active Solver. The InnoCentive CEO, Dwayne Spradlin, blogs about the mission and how the solvers have 'helped changed the world' in the past year. In this blog he gives a great synopsis of what they have done in the last year and discusses some of the most noteworthy Challenges solved in 2011.

Connect with the global Solver community.
InnoCentive is home to a diverse global community of Solvers. Each Solver brings his or her unique experiences to every Challenge. It is recommended to follow the "I'm a Solver" blog section, where they regularly feature posts written by winning Solvers from around the world. You'll learn who they are and what makes them tick. They come from all walks of life and most likely possess many of the attributes that caused you to register with InnoCentive.

Personalize your experience with My InnoCentive.
When you log in to InnoCentive using your username or email and password, you'll be directed to My InnoCentive. From here, you can personalize your profile by clicking on the tabs labeled My Interests, My Account, and My Public Profile found across the top of the page. The My Challenges Tab aggregates all the Challenges you are currently working on, so you can easily keep track of deadlines and Challenge updates. If you have not viewed any Challenges you will be directed to the Recommended Challenges view which will select Challenges based on your indicated interests.

Start solving...view the details of some Challenges.
Each time you view the Details of a Challenge you will be asked to accept the Solver Agreement that is attached to the Challenge. It is by signing this agreement that you open a Project Room for a Challenge and the Challenge Details come into view so you can start working on your solution. From here you can ask questions and submit your solutions.


But how to find a relevant research demand?

You have already read about Fold.it, the site where people play online to solve protein structure for free. Imagine now an online pavillion who is actually paying the intellectual work of scientists working at home through different calls - named Challenges - to take part in a real scientific problem. This is InnoCentive. There are different challenge calls on InnoCentive: the theoretical one, the analytical one, etc. Take a look on their page where they are briefly explained. Each challenge is defined and written up by one innovation manager in collaboration with the seeker posting the challenge. Usually, InnoCentive offers problems and awards from highly reputable seeker companies and not-for-profit organizations, such as Procter & Gamble, Eli Lilly, and the Rockefeller Foundation. To have an idea of the level of the creativity required to solve a typical challenge, read this Science article excerpt:
This week, Massachusetts-based InnoCentive announced the winners of its latest Web-based challenge: to use smartphones to detect potholes. Building on a city of Boston app called Street Bump, which uses GPS and accelerometer data from a smartphone to record a car's location and sudden bounces, contestants vied to find ways to pool this data from many vehicles while distinguishing potholes from jolt-inducing features like railroad crossings... [from: Science 24 February 2012, page 897]
How can I find a Challenge that might interest me? All the open challenges reside in a Challenge Center whose tab is available from your My InnoCentive page. Different disciplines classify a challenge and some pavilions determines their themes or populations features. You can choose challenges by selecting tags, then sorting them by posted date, deadline, award amount or number of solvers who have opened a project room. At that time you may also request a weekly digest of your selected view sent to your email address.

Do I need to sign an agreement? Yes, but electronically. Each challenge type has different Solver Agreements to be signed. The Seekers, who also have signed agreements and are paying to post their challenges, decide in conjunction with the project manager what challenge type best fits their problem. InnoCentive has been in business since 2001 and has awarded over 7 million dollars to over 850 Solvers. To check out these solvers and previously awarded Challenges you can have a look at the Awarded Challenges page.

Working on a Challenge. So find that challenge you want to solve. For instance, sell how to recover Bacillus spores from swabs at $30,000, or minimize surface damages on chocolate for 20,000 bucks. When you open the corresponding Project Room, all the details of the Challenge will become visible. You will find confidential data that the seekers want to make available to you but do not want to share with everybody. One of the things you do when you sign the Solver agreement is to keep this detailed information private. In the Project Room you will also see a Message and Solution tab. If you need to ask questions about the technical details of a Challenge click on the Message tab and select the Compose New Message button. The manager following this challenge will answer your question or get an answer from the seeker. Click on the Solution tab when you want to submit a solution for reducing fat absorption in french fries, get it accepted and enjoy the $8,000 money reward. Happy searching and solving!