The latest version of the connectome is https://github.com/openworm/PyOpenWorm/blob/master/OpenWormData/aux_data/herm_full_edgelist.csv, right?
In this spreadsheet I can see a gap junction between AVA and AVB (https://github.com/openworm/PyOpenWorm/blob/master/OpenWormData/aux_data/herm_full_edgelist.csv#L6156).
Does this GJ exist in C. elegans? I was told that there should not be a GJ
In this spreadsheet I can see a gap junction between AVA and AVB (https://github.com/openworm/PyOpenWorm/blob/master/OpenWormData/aux_data/herm_full_edgelist.csv#L6156).
Does this GJ exist in C. elegans? I was told that there should not be a GJ
wormwiring.org is an excellent resource for this data
Broadly, C. elegans has 25 innexins. The Altun 2009 paper is a pretty good resource for this data: https://www.ncbi.nlm.nih.gov/pubmed/19621339
The best data for cell-specific transcription is Marie's recent Elife paper:
I think that represents the best data we have to date.
Hope that's helpful!
Meant Marie for transcription factors. For the transcriptome, there are several public data sets, wormbase.org has a ton of annotations, and Lori's new paper with John White does a great job as well in the supplement: http://www.cell.com/current-biology/fulltext/S0960-9822(16)31212-X
Forgot about the history & context of this thread. Re-reading it now & realized we were discussing single-cell RNA-Seq. David Miller is visiting Oliver's lab next week. Provided he has time, if you'd like, I can relay a few questions OpenWorm might have regarding the work they're doing with single cell transcriptomics.
@Eviatar, regarding ion channel genes, the main question is: What is the best gene expression dataset available for adult hermaphrodites to find out ion channel genes being expressed in every specific cell.
For example,
Many Microarray datasets available at GEO lack data for many type of ion channel genes in their chipsets, so, I couldn't find useful data at GEO too.
Finally, I need to know if there is any dataset available that includes all ion channel genes in their chipset samples, and the experiment focus on adult C. elegans!
For example,
egl-19 is a gene encoding an L-Type Calcium channel which has found to be expressed in body wall muscles as well as some neurons, however, I could find only 3 cells that express this gene in the dataset provided by Lori's paper which is not true! (Although, I couldn't find any dataset for the Marie's work!)Many Microarray datasets available at GEO lack data for many type of ion channel genes in their chipsets, so, I couldn't find useful data at GEO too.
Finally, I need to know if there is any dataset available that includes all ion channel genes in their chipset samples, and the experiment focus on adult C. elegans!
@VahidGh Marie's paper provides a table with the TFs that pattern differentiation in each neuron (at least what we know to date). You're looking for something else. It should be noted that the data you're after is split in 2. It's easy to ID non-neuronal cells as they tend have distinct morphology & stereotypy in location. On the other hand, neurons require landmarks for ID and so, ion channels present in neurons with good ID is a very sparse data set (this is likely the vast majority of what you're looking for).
Take a look here: http://www.wormbook.org/chapters/www_neuronalgenome/neuronalgenome.html
You'll notice that for vast families of ion channels (the LGICs for example) so very little is known about their expression.
That is the current state of such work. The data sets that purport to tackle this often present a significant amount of false positives & negatives due to limitations in methodology.
Lori's data set only covers neurons.
In short, what you're looking for doesn't yet exist. Piecemeal data exists. You can collect it using WormMart: http://wiki.wormbase.org/index.php/Data_mining:WormMart
Hope that helps.
One thing, since claims of work being untrue in science are usually viewed as strong accusations, I would urge you to use different language in these scenarios.
Going back to the original comments, I think I see some of the confusion. What I mentioned before is that single-cell transcriptomes are being done now by several labs. What I mean is right now. The data has not yet been published. I know David Miller's lab has been pursuing this. I think Paul Sternberg has been focusing on some of this work as well. When done, this data will have much higher fidelity than what is present in WormBase at the moment ( a collective of published findings, from many different labs, with quite a few errors present due to the difficulty of the work). If you're looking to work with what exists now, you will have to resign yourself to working with what WormBase offers and knowing that this data will change considerably over the next few years.
@Eviatar, Thanks for your comments. It seems like we should consider other approaches for now. Maybe something like pathway analysis would be more reasonable as suggested by @balicea. If taking this approach, then we should look for the best dataset available for this purpose (or the most comprehensive one)!
Also, it seems the WormMart has been replaced with WormMine since 2016.
And regarding how to use true word :), yes, It would be better to say it's not complete for our purpose.
Also, it seems the WormMart has been replaced with WormMine since 2016.
And regarding how to use true word :), yes, It would be better to say it's not complete for our purpose.
@lungd @raminmh @slarson , sorry for the delay but I went back to look at the putative AVA / AVB gap junction. It appears as though this is an ambiguous connection that I had scored. When re-analyzing the EMs I wanted to be as sensitive as possible, and this is a connection that I scored despite the quality of the micrographs in this region. You can see what I scored here: http://imgur.com/a/4v9Bg. AVBL is labeled '4' and AVAR is labeled '3'. This connection was only observed once and only between one of the two bilateral pairs, I would not be absolutely certain this connection is representative of all animals.
Sorry..should be thanks for this!
I just got a message that OpenShift was being sunset and I had a few projects for the openworm project that were running there. Do we need to do anything to move those somewhere? Are they still being used? (pyopenworm-pyopenworm.rhcloud.com, movementvalidation-channelworm.rhcloud.com, channelwormdjango-channelworm.rhcloud.com)
@gmayank32 haven't heard of WPS. What is it?
@mantzaris Is this what you're looking for? http://www.wormatlas.org/neurons/Individual%20Neurons/Neuronframeset.html
will have to dig up more info on the potential activities
