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Ariadne: Guide to Building Networks in Pathway Studio – An Introduction 1

Guide to Building Networks in Pathway Studio – An Introduction

This guide will demonstrate basic steps in building networks for a protein or list of proteins or other entity types.

Please see Ariadne’s Pathway Studio support site for more training materials, including a self-guided Training Manual, Analysis Guides

(showing advanced work flows), and FAQs.

http://www.ariadnegenomics.com/support/pathway-studio-7/

A. Add protein(s) to a new pathway view, select the protein(s) (or other entity types) and open the

advanced building pathway wizard to access the algorithms for building different types of networks.

Open a new pathway view by selecting “New Pathway” from the Information Pane on the left .

Once you have added your desired proteins to the New Pathway view, select the proteins. Selected proteins/entities have a blue ring

around them. Open the Advanced building pathway wizard by selecting: Add > Advanced.

These useful short

cut menus for

building networks

will not be

demonstrated in

this tutorial.

Select the “Home” tab on the top of the

Information Pane to find the link to open a

New Pathway.

See the Training Manual, available on

Ariadne’s support site for more instruction on

how to search the ResNet database to find

entities or to import a list of entities and add

them to the New Pathway view.



B. Select the algorithm most appropriate for the desired resultant network.

C. Select the directionality of the relations, the entity type(s) and relationship type(s) for the desired

network.

Directionality of Relations

The select algorithm type dialog provides you with the

choices to:

· Add Neighbors: find entities directly connected to the

entity / entities selected on the network diagram from the

ResNet database.

· Add direct interactions: find the relationship between two

or more selected entities on the network diagram.

· Add shortest path: find relationships between two or

more selected entities on the network diagram, adding

entities as needed to form the relationship.

· Add common targets: find one or more targets that are

regulated by at least two or more of the selected entities on

the network diagram.

· Add common regulators: find one or more regulators that

regulate two or more of the selected entities on the

network.

· Add Neighbors from a group: find entities directly

connected to the entity / entities selected on the network

.diagram from a specified group.

Screen shot from Pathway Studio Desktop.

Pathway Studio Enterprise dialog also allows for number of common

targets or regulators to be specified.

All relationships, except binding, have directionality.

You can select upstream only relations or

downstream only relations or all relation types

(both).

You can include binding in with all upstream or all

downstream relations by simply selecting binding in

the Relation Type dialog in the following steps of

the wizard.

Next select the desired entity types and relation

types. Selection of network types and relations and

entity types are dependent on the specific biological

question to be answered.


Entity Types

Small Molecule – naturally occurring metabolites in mammalian cells (ResNet Mammal); also drugs and non-naturally occurring in

mammalian cell small molecules and metabolites (ChemEffect).

Treatment – non-chemical treatments and environmental conditions, such as cold shock.

Relation Types

PromoterBinding – a regulator that binds to the promoter of a gene.

ProtModification – a regulator that changes the modification of the target molecule, usually by a direct interaction such as

phosphorylation, glycosylation, acetylation etc.

MolTransport – a regulator that changes the localization of the target (molecular translocation, export, import etc.)

Protein – defined by Entrez Gene (represents both

genes and the gene products – proteins)

Cell Process – biological processes, most

coincide with Gene Ontology (container entity)

Functional Class – most functional classes

coincide with Gene Ontology. (container entity)

Disease – health conditions and disease terms

from MeSH

Complex – several polypeptides that form a

complex via physical interactions (container entity)

Protein, Functional Class and Complex are

frequently grouped together as they represent

overlapping concepts.

.

Regulation – changes the activity of the target by an

unknown mechanism (may be direct or indirect). This

is a less specific relation type than others provided.

ChemicalReaction – enzyme catalyzed reaction

involving small molecules.

Expression – regulator changes protein abundance

by affecting levels of transcript or protein stability.

DirectRegulation – influences target activity by direct

physical interaction (excluding promoter binding

interactions).

MolSynthesis – regulator changes the concentrations

of the target (usually a small molecule target).

Binding – direct physical interaction between two

molecules.


The following section gives some examples of network building work flows but does not show all possibilities of networks that can be built

using Pathway Studio.

D. Examples of biological questions and the wizard pathway building settings used to answer find the

answers in the ResNet database.

1. What are all the known associations with my protein in the ResNet database?

Add protein to pathway view and select.

Wizard settings: algorithm: add neighbors; directionality: both; entity type: check all; relation type: check all.

2. What cell processes is my protein involved in? Add protein to pathway view and select.

Wizard settings: algorithm: add neighbors; directionality: downstream ; entity type: cell process; relation type: regulation.

Style sheet: By Type Style sheet: By Effect (positive/negative/unknown)

The “by type” style sheet

colors relation types for

easy identification.


3. What proteins regulate the expression of my protein? Add protein to pathway view and select.

Wizard settings: algorithm: Add neighbors; directionality: upstream; relation type: expression & promoterbinding ; entity type: protein, or

protein/functional class/complex

proteins only proteins/complexes/functional classes

For ONLY transcriptional regulation use only the relation type “promoterbinding”.

It is common to group “proteins” “complexes” and “functional classes” together when examining protein mediated activities.

4. Do any proteins modify (ex. phosphorylate, dephosphorylate etc.) my protein? Add protein to pathway view and select.

Wizard settings: algorithm: add neighbors; directionality: upstream; relation type: directregulation; entity type: proteins or proteins/functional

class/complex

DirectRegulation describes events where regulation

of a protein (such as modification) occurs through a

direct physical interaction.


5. Do any miRNAs regulate my protein? Add proteins to pathway view and select.

Wizard settings: algorithm: add neighbors from a group - select the desired group (Ariadne Ontology > Molecular Function > miRNA);

directionality: upstream; entity type: proteins; relation type; all

miRNAs are represented as proteins in the ResNet database. See the “Introduction to miRNA Analysis in Pathway Studio” for more

information about working with miRNA data and importing predicted miRNA relations into your database. miRNA regulators can also be

identified through the sub-network enrichment algorithms.

6. Are my proteins associated with any similar diseases? Add proteins to pathway view and select.

Wizard settings: algorithm: add common targets; entity type: disease; relation type: regulation

The “Common targets” algorithm means a target for two or more members of the selected group (desktop).

Common target thresholds can be adjusted for Enterprise users.

Darker lines represent more references for a relation. The higher the number of references for a relation, the more times it is described in the literature and

the more confidence you can have in the relationship.

Style Sheet:

By Type

Style Sheet:

By Reference

Count


7. Are any of the proteins known to be associated with a specific disease also associated with a second disease?

Step 1: Find all the proteins associated with a specific disease. Add disease to pathway view and select.

Wizard settings: algorithm: add neighbors; directionality: upstream; entity type: protein; relation type: regulation

Step 2: Find all connections between the second disease and proteins associated to first disease. Add second disease to pathway view and select.

Choose: Add > Relations between Selected and Unselected.

8. Are any of my proteins known physically interact with each other proteins? Add proteins to pathway view and select.

Wizard settings: algorithm: direct interactions ; directionality: NA; relation type: binding and directregulation (can also include ProtModification);

entity type: NA


9. Are my proteins regulated by any small molecules? Add proteins to pathway view and select.

Wizard settings: algorithm: add neighbors; directionality: upstream; relation type: regulation/moltransport/expression/directregulation;

entity type: small molecule

10. If my proteins have no direct interactions, can I connect them through intermediate entities? Add both proteins to pathway view and select.

Wizard settings: algorithm: add shortest path: directionality: both; relation type: all; entity type: all

Filters can be more specific to identify only connections through specific entity types or through specific relations.

If “Find Shortest Path” is applied to a large number of selected entities, the calculation may take a long time to run.

[Type a quote from the document or the

summary of an interesting point. You can

position the text box anywhere in the

document. Use the Text Box Tools tab to

change the formatting of the pull quote text

box.]

DirectRegulation relations

only shown here.


11. (ChemEffect database only) Does my small molecule regulate any cell processes or diseases? Add small molecule to pathway view and select.

Wizard settings: algorithm: add neighbors: directionality: downstream; relation type: regulation; entity type: cell process and disease

12. (Plant database only) What proteins are associated with a specific plant trait? Add plant trait (cell process) to pathway view and select.

Wizard settings: algorithm: add neighbors; directionality: upstream; relation type: regulation; entity type: proteins

This guide provides an introduction to network building using Pathway Studio and ResNet. For more detailed information on how to use

Pathway Studio please visit our website at: http://www.ariadnegenomics.com/support/pathway-studio-7/

Here you can find a self-guided Training Manual that will provide more detailed information on network building, Analysis Guides

(showing advanced work flows), and FAQs.

If you have any additional questions about Pathway Studio, please feel free to contact Ariadne’s Technical Support at:

[email protected] or call us at 866.340.5040 (US and Canada toll-free) +1.240.453.6301 (Worldwide).

(Network results filtered for relations

with 10 references or greater in this

figure.)

Style sheet: “By Effect”

Plant traits are represented as

cell processes.


mailto:[email protected]

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