Question: Well-Annotated Functional Pathway
8
gravatar for Andrew Su
6.9 years ago by
Andrew Su4.8k
San Diego, CA
Andrew Su4.8k wrote:

The dilemna: I am submitting a grant proposal tomorrow morning. However, inspiration hit this morning and I need to make a new figure on short notice.

The need: My new figure will describe a well-annotated biological pathway. Here are the specific requirements:

  • 10-20 pathway members
  • edges must define functional relationships, not the experimental or analytical technique used to determine the edge (e.g., yeast two hybrid, co-expression, literature cooccurrence)
  • functional edge types that are wanted include (but are not limited to):
    • Transcriptional activation/repression
    • Phosphorylation/dephosphorylation
    • Protein cleavage
    • Glycosylation
    • Methylation
    • Other physical interaction

Note, I'm not looking for someone to identify pathway members, then pull out edges from PPI/coexpression databases. I'm looking for an expert-curated pathway diagram, perhaps from a review article on the topic or perhaps one of the curated pathway databases.

Edit: Networks do not need to be annotated with rate constants and the like. I am interested a qualitative description of a gene network...

Edit: Ideally, I'm looking for a network that has multiple edge types listed above...

The reward: Recognizing the urgency of my request, I'm mortgaging another 250 reputation points for the best answer. However, only answers in the next six hours are eligible. (Note the bounty will be entered in the system as soon as I'm able -- after a few days I think. But again, I need your answers now!)

The bonus: I will add an additional 100 reputation points to the bounty if the pathway is specifically on the Regulatory T cell differentiation pathway.

pathway annotation • 2.5k views
ADD COMMENTlink modified 6.9 years ago by Casey Bergman17k • written 6.9 years ago by Andrew Su4.8k

Biostar is just awesome. That is all...

ADD REPLYlink written 6.9 years ago by Andrew Su4.8k

Thanks to everyone who gave answers. Very helpful! In addition to the specific examples given, I learned (or was reminded) that biocarta.com, reactome.org, cellsignal.com, and qiagen.com are all great resources for beautiful illustrations of well-annotated pathways. Wikipathways (which I love) has great breadth but lacks the artist's touch.

In any case, I'm awarding the bounty to Alex Paciorkowski for the answer that ended up being most helpful for the grant proposal. Thanks all!

ADD REPLYlink written 6.8 years ago by Andrew Su4.8k
4
gravatar for Alex Paciorkowski
6.9 years ago by
Rochester, NY USA
Alex Paciorkowski3.3k wrote:

The 2 very well annotated functional pathways that come to mind for me are (1) the MTOR pathway and (2) the RAS pathway.

Here are some references with figures:

MTOR

Swiech, et al 2008, Zeng, et al 2010

RAS

Tidyman & Rauen, 2009

If the figures are not in the format you wish, you can easily extract the genes involved and build your own figures in Biotapestry for transcription factors, and ProteinLounge or String to show other types of functional relationships.

Hands down, one of the best functional figures I have seen yet is of the synapse.

I don't know of any specific T cell regulatory pathways at my fingertips, as that's not my field of expertise.

Good luck with your submission!

ADD COMMENTlink written 6.9 years ago by Alex Paciorkowski3.3k

Figure 1 of Swiech is pretty outstanding. Good one!

ADD REPLYlink written 6.9 years ago by Andrew Su4.8k

I like MTOR because of its relevance to insulin signaling, diabetes and aging.

ADD REPLYlink written 6.9 years ago by Larry_Parnell16k
3
gravatar for Sean Davis
6.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

You might take a look at wikipathways and reactome.

ADD COMMENTlink written 6.9 years ago by Sean Davis25k
1

thanks for the links. Yes, I'm aware of and love both those sites, but quality does vary. If anyone has specific pathways that they know to be high quality, please submit that as an answer...

ADD REPLYlink written 6.9 years ago by Andrew Su4.8k
3
gravatar for Casey Bergman
6.9 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

Neither are T cell development but these examples from Levine & Davidson (2005) are highly curated and have multiple node types:

1) Endoderm development in the sea urchin:

alt text

OR

2) Dorsal-ventral development in the fly:

alt text

ADD COMMENTlink written 6.9 years ago by Casey Bergman17k
2
gravatar for Madhan
6.9 years ago by
Madhan220
United States
Madhan220 wrote:

Hi Andrew Su,

I often use SigmaAldrich.com site to get the annotated information about the pathways. See if this can be useful to you.

T cell differentiation Pathway:

http://www.sigmaaldrich.com/catalog/ProductDetail.do?&F=CP&ST=YFG&IID=ING:3qbdh

ADD COMMENTlink written 6.9 years ago by Madhan220

You can Zoom in and click on the links to know the type of interaction.

ADD REPLYlink written 6.9 years ago by Madhan220

Thanks for the pointer. Not bad... It identifies the right genes but the edge types are a little more rudimentary than I was hoping to find.

ADD REPLYlink written 6.9 years ago by Andrew Su4.8k
2
gravatar for Mary
6.9 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Something like this? http://www.biocarta.com/pathfiles/h_il7Pathway.asp

ADD COMMENTlink written 6.9 years ago by Mary11k

That one's pretty darn good. The edge types in the figure aren't typed, but the relationships are described in the caption. Nice one, Mary...

ADD REPLYlink written 6.9 years ago by Andrew Su4.8k
2
gravatar for julieN
6.9 years ago by
julieN250
Cambridge, MA USA
julieN250 wrote:

my two cents:

http://www.cellsignal.com/pathways/lymphocyte.jsp

ADD COMMENTlink written 6.9 years ago by julieN250
1
gravatar for Larry_Parnell
6.9 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

I would consider the epidermal growth factor receptor signaling network. This is a go-to pathway in systems biology for those interested in relationships of entities at the biological levels as well as describing those relationships with differential equations. The EGFR pathway is important in development and in cancer.

I do not know a specific citation, but would start with work (original research or review) by Walter Fontana.

ADD COMMENTlink written 6.9 years ago by Larry_Parnell16k
1
gravatar for Larry_Parnell
6.9 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

A second answer - different from the first, mainly because of its familiarity. Try the cell cycle.

There are some nice cell cycle pathways at cellsignal.com. I particularly like the "nodes" of caffiene, DNA, UV light, and the hierarchy of signals leading to a G2 to M transition. The G1/S checkpoint also looks good.

ADD COMMENTlink written 6.9 years ago by Larry_Parnell16k
1
gravatar for ALchEmiXt
6.9 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

Are these qiagen pathways too high meta-level? They are quite illustrative and on many topics including many aspects of T-cell differentiation and maturation... (not including the specifics of actions usually though (edit: see keys since they do... my bad)

e.g. https://www.qiagen.com/geneglobe/pathwayview.aspx?pathwayID=240

Keys: https://www.qiagen.com/geneglobe/help/pathwaykey.aspx

Other pathways at qiagen: https://www.qiagen.com/geneglobe/pathways.aspx

ADD COMMENTlink written 6.9 years ago by ALchEmiXt1.9k

The Qiagen pathways were all done by the protein lounge team so you may want to go to http://www.proteinlounge.com to get the most currently updated pathways.

ADD REPLYlink written 6.6 years ago by proteinlounge0
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