C Elegans gene expression datasets available?

[Shreejoy Tripathy]

Hello all,

First time poster here, long time OpenWorm admirer.

Are there gene expression data sets available which characterize the genes expressed by some or all of the neurons in c elegans?  

I've been thinking that given the difficulty in recording from c elegans neurons directly due to technical reasons, perhaps a better approach would be to infer the ion channel distributions expressed by each neuron not from neuron voltage recordings, but from the genes expressed by each neuron?  Like discussed in this paper: http://cercor.oxfordjournals.org/content/14/12/1310.abstract; pdf:  

https://www.dropbox.com/s/7r51vkamdo7izbg/Toledo-Rodriguez%20et%20al.%20-%202004%20-%20Correlation%20Maps%20Allow%20Neuronal%20Electrical%20Propert.pdf

Just a thought.

[Giovanni Idili]

Hi Shreejoy! 

Your idea is intriguing and thanks for sharing the paper. 

We have some calcium traces from the Leifer lab I believe but it's been hard to do something with them. 

I'll let the guys who have been working on that stuff reply!

[InterIntelligence Research]

Shreejoy:

 

There are gene expression data sets out there for C Elegans and I've been half heartedly looking to see how we can integrate into our own database but have not taken this step yet. What you are saying is true; i.e. the Gene does express the type of neuron transmitter and receptor, the type of innexins that make up the neuron. My dream has always been to use the genes to create and simulate the entire organism so we are on the same page.

 

The attached spreadsheet is a worksheet I have been working with off and on for a while. Note the tabs to take you to various data sets.

 

Hope this helps,

 

Tim

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[Chris Jensen]

Thanks for the paper, looks like a good one. 

At the very least, matching against the genome will provide a sanity check for other results. I have just begun to (attempt) cataloging all the ion channels. My search so far leads me to believe that a good bit of the information needed for the purposes of a neural simulation at this level does not exist in an immediately useful form and will need to be inferred from available results and data. Of course, I could just be missing some critical database that would make life easy.

[Shreejoy Tripathy]

I have just begun to (attempt) cataloging all the ion channels

Does that mean you guys know which ion channels are expressed by which neurons in c elegans?  

Also, I want to make sure that I'm being clear about a genome versus knowing the genes which are expressed by each neuron.  A genome tells you what genes are available to each cell (genomes are typically the same from cell to cell) whereas what makes cells different are the genes which expressed (i.e., turned on and off) and eventually turned into proteins.

[InterIntelligence Research]

Chris:

 

There is a plethora of information regarding ion channels, just google "C Elegans Ion Channels" and it's obvious. What I find difficult about defining Ion Channels is we talk about the ion and the effects of the channel but there seems be a lack of properties and for simulation purposes, the electrical properties would be valuable. For instance, I know MEC-4 is a sodium channel but I don't know much about voltage changes or the proteins that open the channel, etc., and these properties probably most likely change depending on the neural connection, the stimuli and the homeostatic state of the worm (e.g. is it starving or quite full). I'm sure the data is out there and we need to dig it out. In addition, we know of instances where values have been applied and later recounted so it also takes some time to make sure that these values have not changed over time with further experimentation. It would be very valuable to dig up as much information as you can on motor connections for the place we are at now for our simulation. Attached is a paper that has a section that has several references to data sources that might help propel you.

 

Best of luck to you, there's a lot of work here and I greatly appreciate your contributions. Anything I can do to help, I will.

 

Thanks

 

Tim

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[Chris Jensen]

On Thursday, October 10, 2013 4:39:54 PM UTC-5, Shreejoy Tripathy wrote:

Does that mean you guys know which ion channels are expressed by which neurons in c elegans?  

There is this paper: http://www.wormbook.org/chapters/www_neuronalgenome/neuronalgenome.html

That contains a wealth of information directly relevant to the topic. Unfortunately, if you scan down to the tables you will notice a large number of question marks in the columns indicating where the genes are expressed. Completely absent is topological information relative to the neuron, e.g., NCA-1 has been shown to be isolated to axons. Also missing is anything that would guide me toward a bulk electrical model or a molecular level electrochemical model. So far I have found bits and pieces in the numerous papers on the topic, but it all needs to be converted to a consistent form and consolidated.

[Chris Jensen]

Tim,

Thanks for the paper. I will give it a thorough read later, but I can already tell it will be very useful to me. I am still in collection mode, skimming papers and saving them in rough categories for later. There is a very, very large quantity of research and I am still trying to assimilate.

-Chris

[Shreejoy Tripathy]

There is this paper: http://www.wormbook.org/chapters/www_neuronalgenome/neuronalgenome.html

Very cool.  

So far I have found bits and pieces in the numerous papers on the topic, but it all needs to be converted to a consistent form and consolidated.

About how many papers do you think contain this info? like 1000? 100? I may be able to help out - my research is on text mining and neuron properties.

Completely absent is topological information relative to the neuron, e.g., NCA-1 has been shown to be isolated to axons.

For sure, topological information on gene expression distribution is important, but to me, the first thing to know is which genes are expressed in which neurons.

[InterIntelligence Research]

Chris:

 

It is a huge undertaking and from your previous posts, you see clearly what we are up against - great papers/information but just a bit shy of the details. My hope always is by putting a few of these papers together, we get the whole picture. There was a team that wrote a "spider" which would crawl through the PDFs and gleam information based on key words. I started to explore this a bit from a web perspective, having written spiders before, but never got it off the ground.

 

Again, anything you want to ask me or us to do to propel your work, please don't hesitate,

 

Tim

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[Shreejoy Tripathy]

Right!

My sense is that it'd be relatively straightforward to write something that just searched for the keywords c elegans, the names of neurons, and the names of genes.

[Chris Jensen]

There are on the order of a few thousand relevant papers.

1,020 results from PubMed. The search entered was simply: elegans ion channel 

http://www.ncbi.nlm.nih.gov/pubmed/?term=elegans+ion+channel

Scroll down a little. On the right is the exact search that was interpreted by their system and executed. 

5,326 results in the PMC catalog, also from the NIH http://www.ncbi.nlm.nih.gov/pmc/?term=elegans%20ion%20channel

Again, the exact terms the engine executed are on the right.

2,586 results Over at Wormbase (http://www.wormbase.org/resources/paper#1-0-5) for search: ion channel

22,573 results at mendeley for search: +"C. elegans" ion channel

http://www.mendeley.com/research-papers/search/?query=%2B%22C.+elegans%22+ion+channel

Tweaking the search terms obviously will net you broader or narrower results. The NIH catalogs seem to yield references that are mostly of high relevance with a simple search. Mendeley requires some fiddling to come up with the appropriate set of terms and limiters to get a list that is narrow enough to be useful. For example, tweaking the search to: +"C. elegans" ion +channel   (note the extra '+' before 'channel')

narrows the results to 1,016 http://www.mendeley.com/research-papers/search/?query=%2B%22C.+elegans%22+ion+%2Bchannel

There are other catalogs and search methods that I haven't tapped into yet.

[Shreejoy Tripathy]

Very cool.  If you or anyone else is at all interested in using some text-mining to get these references together (even for a first pass which could be refined later), let me know.  I have a lot of code that can probably help.

[Stephen Larson]

One more resource that is notable because it indexes the full text of papers specifically on c. elegans is:

http://www.textpresso.org/celegans/

Currently, this site contains information about the following literatures and data types (data count in parenthesis):

C. elegans: abstract (41978), acknowledgments (9359), body (6450), conclusion (2362), discussion (9005), introduction (15562), materials (10694), references (13636), results (10448), title (45223)

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