Question: Cell Type Marker Databases?
9
gravatar for Adam Cornwell
8.3 years ago by
Adam Cornwell420
United States
Adam Cornwell420 wrote:

Hi, I've been looking to see if there is any kind of public database or resource for cell type-specific markers. These would include genes for proteins that can uniquely identify a cell population using techniques such as FACS. I've tried a variety of different search terms, but haven't managed to come up with much. I figured I would check here to make sure I may not be missing something out there before resorting to literature mining and meta-analysis of GEO data. So far the best I have found are lists of sequences used in commercial cell type validation PCR arrays, for which no citations are given...

Thank you

database • 11k views
ADD COMMENTlink modified 12 weeks ago by Ashwini Patil10 • written 8.3 years ago by Adam Cornwell420
2
gravatar for of
24 months ago by
of20
Stockholm
of20 wrote:

Here is one such marker database:

https://panglaodb.se/markers.html

ADD COMMENTlink written 24 months ago by of20
1
gravatar for Malachi Griffith
8.3 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

For immune (and other) cell types you could start with some resources related to human clusters of differentiation, used in Immunophenotyping. Wikipedia has a decent list of CD molecules. This CD Antigens Table is a fairly rich resource.

There are also specific projects that seek to characterize the distinguishing genes of each tissue. For example the Human Protein Atlas, and the Mouse Atlas of Gene Expression.

ADD COMMENTlink written 8.3 years ago by Malachi Griffith18k
1
gravatar for Ashwini Patil
12 weeks ago by
Japan/Tokyo/Combinatics Inc.
Ashwini Patil10 wrote:

Try CellKb https://cellkb.combinatics.com. It contains about 19,000 cell type signatures manually collected from literature and extensively curated.

We are making mouse cell type signatures available for free for one month. Please get in touch with me for extended access.

ADD COMMENTlink written 12 weeks ago by Ashwini Patil10

Wow, a commercial database for this. I have no idea how this would work for a research project. Say you use this database in a paper, no one else could reproduce the results? Also, this doesn't answer the question, like all of us, the question was about a public database, because we want to build algorithms and run this on our dataset. With this closed-access commercial database none of this would work. Also, without any comparison of a commercial database against other resources, why would anyone buy it?

ADD REPLYlink written 12 weeks ago by Maximilian Haeussler1.3k

CellKb is a collection of marker gene sets published in literature and uses a rank-based overlap method to identify gene sets that match a query gene list in your search. You can download the list of marker gene sets that match with your query list from CellKb along with the source publication. This will allow others to reproduce the results.

CellKb tries to address several issues with existing public databases. Please see my review on Medium for more details: https://medium.com/@ashwini_21267/simplifying-cell-type-identification-in-single-cell-experiments-ca7af7382e51.

Unfortunately, CellKb is not a public database because we have no academic or government funding. But it is very reasonably priced so students and academicians can afford a license. Also we are happy to collaborate with labs for specific research projects, and provide them access to the data.

Please let me know if you or your lab are interested in collaborating with us. I will be happy to give you a demo of CellKb and its features. We are releasing CellKb 2.0 with additional cell type marker sets and features by the end of August 2020!

ADD REPLYlink written 5 weeks ago by Ashwini Patil10

I do not know an example of a successful biological database that is sold commercially for the reasons outlined above. I don't think there is a business model with biological databases. The only one I know who is making money is HGMD, but they provide a free academic version (always last year's and reduced information). No matter how good your database, academic will not buy it. I would recommend making a free version available and forseee a way to make the free version downloadable from pipelines with a wget command (and maybe a token or login or something).

ADD REPLYlink written 5 weeks ago by Maximilian Haeussler1.3k

Those are all very pertinent points and excellent suggestions. As an ex-academic myself, I actually agree with you. Ideally, I would like CellKb to be freely accessible to as many academics as possible and I am trying to figure out a model that will make it sustainable over the long term.

ADD REPLYlink written 5 weeks ago by Ashwini Patil10

As for examples of cases where this has worked, you can look at the licenses of OMIM, UCSC Genome Browser, Genomenom and HGMD, there may also be others, this list is not comprehensive. BIND used to be one, as was TRANSFAC, but I'm not sure about their status now. Usually there is either a fully public version but with warning that it can't be used for commercial research, click-through licenses or limited versions (stripped or outdated) for academic researchers. OMIM generates a unique download link to the files, so they always know who generated the link originally. Commercial publishers also leave hidden watermarks in the PDFs they generate, so if they find a version used commercially, they know the user account from where it was downloaded.

ADD REPLYlink written 5 weeks ago by Maximilian Haeussler1.3k

Thanks for the examples. That helps!

ADD REPLYlink written 5 weeks ago by Ashwini Patil10
0
gravatar for Khader Shameer
8.3 years ago by
Manhattan, NY
Khader Shameer18k wrote:

If you are looking at humans, I would consult Human Proteinpedia (See this page for data categorized using annotations and experimental platforms) and Human Protein Atlas before starting a de-novo literature curation or meta-analysis.

ADD COMMENTlink written 8.3 years ago by Khader Shameer18k
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