Www.reactome.org March 2013 1 A Database of human biological pathways Steve Jupe - [email protected].

www.reactome.org March 20131

A Database of human

biological pathways

Steve Jupe - [email protected]


Background

• Cells contain thousands of molecules, – proteins and small chemical compounds

• They work together to perform tasks. – provide energy

– produce materials

– respond to the environment.

• Processes require coordinated efforts– like a factory production line.

– Biologists refer to a chain of connected molecular events as a pathway.

ELLS 2011


Different types of pathways

• Metabolic networks – provide the energy and materials

• Signaling networks – sense the outside, coordinate activities within and between cells

• (Gene) regulatory networks – control processes, set limits, control the molecular composition of cells

ELLS 2011


The scale of pathways

• Early pathways were pieced together by studying biochemical reactions of individual proteins, measuring the activity, learning the substrates and products, joining them to the next enzyme in the pathway.

• New technologies allow simultaneous measurement of tens of thousands of different molecules.

• This reveals that many biological pathways are interconnected, more complicated than the typical textbook examples, with fluid boundaries. They can work together or against each other (feedback and regulation).

• Scientists who study or interpret these large scale interactions sometimes refer to the field as ‘systems biology’

• When multiple biological pathways interact = a biological network.

• When all possible interactions are added, pathways become extremely difficult to understand

• Biologists often work with ‘canonical’ pathways, those that represent the well-understood part of the entire network.

ELLS 2011


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 reuse it?


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

Rationale - Figures A 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 by Reactome 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 other species

Reactome is…


human

PMID:5555 PMID:4444

mouse

cow

Direct evidence

Direct evidence

Indirect evidence

PMID:8976

PMID:1234

Using model organism data to build pathways – Inferred pathway events


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

CATALYST


Human pathway

PMID:5555 PMID:4444

mouse

cow

Direct evidence

Indirect evidencePMID:8976

PMID:1234

Evidence Tracking – Inferred Reactions


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(more on this later)

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

Lists available from Downloads

See Readme document for more details


Coverage – Content, 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


Tutorial

Tutorial handouts in your info packages…


Front Page http://www.reactome.orgS

ide

bar Main

text

Navigation bar


Exercise 1

…see the Tutorial handouts


The Pathway BrowserSpecies selector

Diagram Key

Sidebar

Pathway Diagram Panel

Details Panel (hidden)

Zoom/move toolbar

Thumbnail


Pathways tab – pathway hierarchy

PathwayReactionBlack-box


Exercise 2

From the homepage, search for ‘PDGF 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 Processing of classical PDGFs?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, protein sets, mixed sets or complexes. Ovals are small molecules (or sets of) 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



Navigating in the Pathway Browser I

Click here

Highlights

Details here

Click here to open pathway diagram...

Home and Analyze buttons


Details here

Navigating in the Pathway Browser II

Click here

ZoomHighlights


Exercise 4



The Details Panel


Exercise 5



Pathway Analysis


Pathway Analysis – Overrepresentation

‘Top-level’

Reveal next level

P-val


Exercise 6

Check this!



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



New Look Browser


End


BioMart – selecting your dataset


BioMart – filters


BioMart – attributes

Check to get

attribute


BioMart – results


Exercise 10

Www.reactome.org March 2013 1 A Database of human biological pathways Steve Jupe - [email protected].

Documents

canonical pathways

multiple biological

cellular compartment

thousands of molecules

biological network

molecules of procaspase

key initiator caspase

deathreceptor pathway