Www.reactome.org Murcia - 3 February 2011 1 A Database of human biological pathways Bijay Jassal.

www.reactome.orgMurcia - 3 February 20111

A Database of human biological pathways

Bijay Jassal


Rationale – Journal informationNature 407(6805):770-6.The Biochemistry of Apoptosis.

“Caspase-8 is the key initiator caspase in the death-receptor pathway. Upon ligand

binding, death receptors such as CD95 (Apo-1/Fas) aggregate and form membrane-

bound signalling complexes (Box 3). These complexes then recruit, through adapter

proteins, several molecules of procaspase-8, resulting in a high local concentration of

zymogen. The induced proximity model posits that under these crowded conditions, the

low intrinsic protease activity of procaspase-8 (ref. 20) is sufficient to allow the various

proenzyme molecules to mutually cleave and activate each other (Box 2). A similar

mechanism of action has been proposed to mediate the activation of several other

caspases, including caspase-2 and the nematode caspase CED-3 (ref. 21).”

How can I access the pathway described here and maybe reuse it?


Nature. 2000 Oct 12;407(6805):770-6.The biochemistry of apoptosis.

Rationale - FiguresA picture paints a thousand words…

but….• Just pixels• Omits key details• Assumes• Fact or Hypothesis?


Reactome is…

Free, online, open-source curateddatabase of pathways and reactions in human biology

Authored by expert biologists, maintained byReactome editorial staff (curators)

Mapped to cellular compartment


Extensively cross-referenced

Tools for data analysis – Pathway Analysis, Expression Overlay, Species Comparison, Biomart…

Used to infer orthologous events in 20 non-human species

Reactome is…


Theory - Reactions

Pathway steps = the “units” of Reactome

= events in biology

TRANSPORTCLASSIC

BIOCHEMICAL

BINDING

DISSOCIATION

DEGRADATION

PHOSPHORYLATION

DEPHOSPHORYLATION


Reaction Example 1: Enzymatic


Reaction Example 2: Transport

REACT_945.4

Transport of Ca++ from platelet dense tubular system to cytoplasm


Other Reaction Types

Binding

Dimerization

Phosphorylation


Reactions Connect into Pathways

OUTPUTINPUT

CATALYST

OUTPUTINPUT

CATALYST

INPUT OUTPUT

CATALYS

T


Human pathway

PMID:5555 PMID:4444

mouse

cow

Direct evidence

Indirect evidencePMID:8976

PMID:1234

Evidence Tracking – Inferred Reactions


Data Expansion - Link-outs From Reactome

• GO • Molecular Function• Compartment• Biological process

• KEGG, ChEBI – small molecules• UniProt – proteins• Sequence dbs – Ensembl, OMIM, Entrez Gene,

RefSeq, HapMap, UCSC, KEGG Gene• PubMed references – literature evidence for events


Species Selection


Data Expansion – Projecting to Other Species

A + ATP A + ADP-PB

Human

A + ATP A + ADP-P

BMouse

BA

Drosophila

Reaction notinferred

No orthologue - Protein not inferred

+ ATP


Exportable Protein-Protein Interactions

Inferred from complexes and reactions

Interactions between proteins in the same complex, reaction, or adjoining reaction

Lists available from Downloads

See Readme document for more details


Coverage – Current TOC

And many more...


Planned Coverage – Editorial Calendar


Reactome Tools

Interactive Pathway Browser

Pathway Mapping and Over-representation

Expression overlay onto pathways

Molecular Interaction overlay

Biomart


Arabidopsis Reactome

http://www.arabidopsisreactome.org/


Tutorial


Front Page http://www.reactome.org

Main text

Navigation bar


Exercise 1


The Pathway BrowserSpecies selector

Search & Analyze barSidebar

Pathway Diagram Panel

Details Panel (hidden)Thumbnail


Pathways tab – pathway hierarchy

PathwayReactionBlack-box


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?2.How many reactions are in the first of these sub-pathways?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.


The Pathway Browser - Pathway Diagrams

Boxes are proteins, sets or complexes. Ovals are small molecules.Green boxes are proteins or sets, blue are complexes.

Catalyst

Input

Outputs

Compartment

Reaction node

Transition Binding Dissociation Omitted Uncertain

Regulation+ve -ve


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’?

2. 2. What symbol represents the reaction ‘Transport of Ca++ from platelet dense tubular system to cytoplasm’? What subtype of reaction is this?

3. 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?


Navigating in the Pathway Browser I

Click here

Highlights

Details here

Click here to open pathway diagram...

Home and Analyze buttonsSearch


Highlights

Details here

Navigating in the Pathway Browser II

Click here

Zoom


Exercise 4


The Details Panel


Exercise 5


Pathway Analysis


Pathway Analysis – Overrepresentation

‘Top-level’

Reveal next level

P-val


Exercise 6

Check this!

1. What is the most significantly over-represented top-level pathway for this dataset?

2. How many genes are in this pathway, and how many were represented in the dataset?

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)

4. Can you interpret these results in terms of the underlying biology? (Hint: good luck, there are many correct answers!)


Species Comparison I


Species Comparison II

Yellow = human/rat Blue = human onlyGrey = not relevantBlack = Complex


Exercise 7


Expression Analysis I


Expression Analysis II ‘Hot’ = high‘Cold’ = low

Step throughData columns


Exercise 8


Molecular Interaction Overlay


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? 2.How many times has the interaction between FADK1 and Tumor endothelial marker 6 been documented? Hint: This detail is not in Reactome.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?4.Display interactors for UNC5B (bottom left of the cytosol). What happens and why?5.What is the easiest way to remove interactors?


BioMart – selecting your dataset


BioMart – filters


BioMart – attributes

Check to get

attribute


BioMart – results


Exercise 10


The End

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