Answers to Exercises
The answers may change as more data is added to Reactome; these are
based on the June 2010 Reactome release.
Exercise 1
1. Mar 20, 2011: Reactome will be taking part in GSoC 2011
2. Found under Content, Statistics 5274
3. Found under Content, Editorial Calendar. June 2011
4. First topic is Post-translational modification - Acylation
Exercise 2
From the homepage, search for ‘Notch signaling’.
Click on the top pathway hit. This will open it in the Pathway Browser.
Ignoring the diagram for now, look at the Pathways tab on the left.
1. How many sub-pathways does this pathway have?
The top pathway hit is ‘Signaling by Notch’. This has 7 subpathways, revealed by clicking the + symbol to the left of the
pathway name.
2. How many reactions are in the first of these sub-pathways?
The first subpathway ‘Transport of Notch receptor precursor to
golgi’ has 4 reactions.
3. What reaction follows Notch 2 precursor transport to Golgi?
Hint: If it’s not visible, open the Details pane at the bottom of the
page by clicking on the blue triangle.
It’s tempting to think it will be the next reaction down in the
hierarchy, and often this is the case, but not for this reaction. The
hint suggests opening the Details pane. One of the details is
Following events: this will always correctly identify the next reaction
step in a pathway. The answer is ‘Notch 2 precursor cleaved to
form a heterodimer’. An alternative way to identify preceding and
subsequent reactions is to follow the connecting lines on the
pathway diagram.
This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of
this license, visit http://creativecommons.org/licenses/by-sa/3.0/ or send a letter to Creative Commons, 543
Howard Street, 5th Floor, San Francisco, California, 94105, USA.
1
Exercise 3
From the Homepage, search for the pathway ‘Effects of PIP2 hydrolysis’
and open it in the Pathway Browser.
1. What symbol represents the reaction for ‘Binding of IP3 to the IP3
receptor’?
The reaction node for this reaction is a solid circle, representing a
binding reaction.
2. What symbol represents the reaction ‘Transport of Ca++ from
platelet dense tubular system to cytoplasm’? What subtype of
reaction is this?
The reaction node symbol for this reaction is an open square,
representing a ‘transition’ reaction. It is a transport reaction.
3. What is the catalyst (descriptive name) for ‘2-AG hydrolysis to
arachidonate by MAGL’? Can you find its UniProt ID and name the
two outputs of this reaction?
You could drag the diagram around to find this reaction, but it’s
easier to use the pathway hierarchy. This reaction is in a
subpathway of Effects of PIP2 hydrolysis, Arachidonate production
from DAG, so first you have to open the subpathway with the +
symbol. Click on the reaction name to find it in the diagram. The
descriptive name for the catalyst is the label for the catalyst object,
Monoglyceride lyase. To find the uniprot ID click on monoglyceride
lyase to see details in the Details pane – the uniprot ID is listed as
Reference entity – Q99685. Click on the reaction node to find see
details of the reaction in the Details pane, outputs are Arachidonate
and Glycerol.
Exercise 4
Open the pathway Apoptosis in the Pathway Browser.
Select the sub-pathway box “Intrinsic Pathway in Apoptosos”
1. How do you open the pathway diagram for this sub-pathway?
Left-clicking to select the sub-pathway object for ‘Intrinsic Pathway
for Apoptosis’ does not open the diagram. To do this either a)
Right-click and select the option Go To Pathway, or click on the
sub-pathway name, highlighted in the pathway hierarchy on the
Pathways tab.
2. With this pathway diagram open, what happens if you click on the
sub-pathway “BH3-only proteins associate with and inactive
antipoptotic BCL-2 members”?
2
‘Intrinsic Pathway for Apoptosis’ has sub-pathways, click on the +
symbol to reveal them. When you click on the sub-pathway ‘BH3only proteins associate with and inactivate anti-apoptotic BCL-2
members’ the 3 reactions in this sub-pathway are selected on the
pathway diagram, indicated by green boxes around the reaction
nodes.
3. What happens if you click on the reaction “Sequestration of tBID by
BCL-2” in the pathway hierarchy?
Clicking on ‘Sequestration of tBID by BCL-2’ will select just this
reaction, but also centres the pathway diagram on this reaction
(unless you are zoomed out – if you were try zooming in and drag
the diagram so you can’t see this reaction, then click on it in the
hierarchy again).
Exercise 5
1. 'Activated type I receptor phosphorylates R-SMAD directly is part of
the pathway ‘Signaling by TGF beta’.
2. The answer to this question is in the Details pane if you click on the
reaction in the pathway hierarchy, under Cellular compartment –
plasma membrane. (Current reactome says
3. The associated GO molecular function is ‘transmembrane receptor
protein serine/threonine kinase activity’.
4. The reference is Souchelnytski et al. 2002.
5. Yes for dogs, not for yeast, can be answered by looking at the
detail ‘Equivalent event(s) in other organism(s)’
Yeast name: Saccharomyces cerevisiae
Dog name: Canus
3
Exercise 6
1. What is the most significantly over-represented top-level pathway
for this dataset?
Gene Expression
2. How many genes are in this pathway, and how many were
represented in the dataset?
411 genes in the pathway, 174 represented.
3. Why is the top-level pathway Chromosome Maintenance higher in
the list than Signalling by Wnt when the latter has a more significant
probability score? (Hint – use the Open All button)
Chromosome Maintenance is higher in the list than Signalling by
Wnt because the former has a sub-sub-sub-pathway, Telomere Cstrand (Lagging Strand) Synthesis that has a more significant
probability score than that of Signaling by Wnt. The top-level
pathway inherits this from the sub-pathway, pushing it up the list.
4. Can you interpret these results in terms of the underlying biology?
(Hint: good luck, there are many correct answers!)
Any answer that suggests ‘something that increases cell growth
and division’ is correct!
Exercise 7
4
1. Complement factor B is yellow, indicating that it has been inferred
to exist in rat.
2. You can answer this by clicking on the box for Complement factor B
and looking at its details – look for ‘Entities deduced on the basis of
this entity’ – this lists the other species that have been inferred to
have Complement factor B.
3. Complement factor 2 is blue, indicating that it has not been inferred
to exist in rats.
4. C3b is black because it is a complex. Right-click on it and select the
option ‘View participating molecules’ to see which are predicted to
exist in rat. They are 2 components, both blue, so not predicted to
exist in rat.
5. Calcium is grey because it is a small molecule, so species
comparison is not relevant. Other pathway objects that have no
Uniprot ID will also be grey.
Exercise 8
1. 49 proteins in the pathway,
2. 45 have expression values in the dataset.
3. It’s easier to see this if you zoom out so all the pathway is visible. I
think it’s HR23B, top left of the diagram, but I have not checked all
the complexes...
4. Find the complex in the top right then right click to Display
molecules. The reddest one is:
DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide
(RPB17)
5. The probe ID is displayed if you mouse over the cell, it was the
identifier used in this dataset – 209302_at.
5
Exercise 8B
Open the chemical structure drawing programme from the Tools menu.
1. Draw the structure for testosterone? Hint: Use the templates button
on the bottom right of the structure drawing programme.
Use the templates – it is the bottom right hand corner.
2. Find all compounds which contain testosterone in their structures?
Hint: Use the “Find compounds which contain” option.
There are 31 compounds in Reactome which contain testosterone.
3. Click on 11-deoxycortisol (CHEBI:28324), how many pathways are
associated with this compound?
There are 7 pathways associated with this compound.
Exercise 9
Open the pathway diagram for Netrin-1 Signaling.
1. Find the protein FADK1 (top centre of the cytosol). Right click on it
and select Display Interactors. How many are there?
FADK1 has 13 interactors.
2. Find the interaction between FADK1 and Lymphoid nuclear protein
related to AF4. What is the interaction detection method used to
determine this interaction? Hint: This detail is not in Reactome.
Click on the line between FADK1 and Lymphoid nuclear protein
related to AF4 to open a page describing the interaction at the
source database, IntAct. This interaction has been identified using
the two hybrid pooling approach.
3. Find the protein SRC (to the left of FADK1). Display interactors for
this protein. How many are there? Can you get a list of them?
SRC has more than 50 interactors, indicated by 50+ in the
interaction count box (you need to be zoomed in to see this). You
can see these 50 in the table within the Analyze, Annotate &
Upload panel; if you export the interactions you will get all
interactions available from the selected source, in this case IntAct.
4. Display interactors for UNC5B (bottom left of the cytosol). What
happens and why?
UNC5B has no interactors, a prompt tells you this.
5. What is the easiest way to remove interactors?
6
There is a Clear button in the Analyze, Annotate & Upload panel.
Exercise 10
Click on Choose Database and select Reactome, then click on Choose
Dataset and select Pathway.
Add a Filter, limiting to pathways containing a list of IDs, select Uniprot IDs
from the dropdown list, enter P17480 in the box. The query returns 9
pathways.
Copy the Pathway Stable ID, REACT_2232, change the filter so it limits by
Pathway Stable ID, enter REACT_2232 in the box. Add the Attribute
Protein UniProt ID. You should have 2 results returned.
You will be asked to save your chosen download format to your computer.
2 lines of output.
7