Cytoscape in Plant Systems Biology

Cytoscape in Plant Systems Biology

Cytoscape in Plant Systems Biology

Resources in Mircoarray

GEOIn-silico Db

Part of NCBIPart of GenomeSpace

Contain microarray datasets onlyContain processed Microarray & RNA-seq datasets

GEO2Enrichr in analysisGenePattern in analysis

You can search any microarray dataset in both using GSE accession.

Microarray analysis tools

GEO2EnrichrGenePattern

Chrome extensionApp in GenomeSpace

Very fastNeeds some time

Can't upload your expression filesCan upload your expression files

No need to download the expression fileNo need to download the expression file

Why Cytoscape ??

Free network analysis tool

Open-source

Related databases are public

Search a gene-list in more than 15 database at once

Cytoscape interface

Import a new network using genelist

1-file >import>network>from public database

2-paste the gene-list

3-click search

4-choose the desired database based on your biological question.

5-select don't merge

KEGG PATHWAY

How to search KEGG pathway online

1-open KEGG pathway site :
http://www.genome.jp/kegg/pathway.html

2-Click on the Organism to choose your organism, a pop-up will appear.

3-write the first name of the organism and choose from menu, press ok.

4-you can simply click search to list all pathways related to this organism

or write gene , metabolite or a process.

5- choose a pathway

Try to search Glycolysis in Apis Mellifera as your organism !!

Glyscolysis Pathway

Compound list in Glyscolysis Pathway

Gene list in Glyscolysis Pathway

KEGGScape

an app to provide comprehensive support for KEGG database

How to import KGML with KEGGscape

Install

KEGGscape app is available from Cytoscape App Manager.

To install KEGGscape, you just need to open the manager (Apps --> App Manager) and select KEGGscape from the middle box.

Load KEGG Pathway Files

Where are the KGML Pathway files?

KGML files are available from KEGG web site:

http://www.kegg.jp/kegg/pathway.html

Open the KGML file in Cytoscape :

File >Import >network>file

And choose the KGML file path ,the network will appear !

Plant Metabolic Network (PMN)

Plant Metabolic Network (PMN)

network of plant metabolic pathway databases

from the literature and computational analyses

http://www.plantcyc.org/

PlantCyc

manually curated or reviewed information about shared and unique metabolic pathways present

over 350 plant species.

How to get a pathway specific to my plant in Cytoscape ?

1-Browse PlantCyc for your organism
http://www.plantcyc.org/about/plantcyc_species.faces

2-click on your organism for example Atropa Belladonna

3-Choose the pathway you wish to download you can use ctrl +f to search

4-Under Operation in the up right ,choose BioPax3>> a file will be downloaded

5-in Cytoscape:
File>>import>>network>>from a file then choose OK

iPATH

iPathDB contains pathways of 52 insects, including six orders, Coleoptera (2), Diptera (23), Hemiptera (5), Hymenoptera (10), Lepidoptera (10), Phthiraptera (1) and Phasmatodea (1).

PlantSEED

Searching SEEDviewer

http://pubseed.theseed.org/seedviewer.cgi?page=OrganismSelect

Need registration

EcoCyc

Orthology search by g:Orth

a tool for mapping orthologous genes in related organisms.

Ortholog genes are similar in sequence and are likely conserved through evolution since a common ancestor. Orhologous genes may also carry out similar function and are therefore relevant in functional analysis.

How to find orthologos gene-list using g:orth ?

1-open g:orth site :

http://biit.cs.ut.ee/gprofiler/gorth.cgi

2-choose the organism which your gene-list belong to.

3- choose your target organism you wish to convert the gene-list.

4-paste your gene-list in the Query

5-click Find orthologos

Enrichment Map

Pathways of pathways

Cytoscape plugin for functional enrichment visualization

In this way, mutually overlapping gene-sets cluster together, making interpretation easier

Steps for g:profiler Enrichment Map

Go to g:Profiler website - http://biit.cs.ut.ee/gprofiler/

Select and copy all genes in the tutorial file

In Options, check Significant only, No electronic GO annotations

Set the Output type to Generic EnrichmentMap

Show advanced options

Set Min and Max size of functional category to 3 and 500 respectively.

Select 2 for Size of Q&T

On the right panel, choose the Gene Ontology Biological process and Kegg and Reactome

Set Significance threshold to Benjamini-Hochberg FDR

Click on g:Profile! to run the analysis

Step 2: Generate Enrichment Map with g:Profiler Output

1. Open Cytoscape

2. In the menu bar, locate the App tab and then select --> EnrichmentMap --> Create Enrichment Map

3. Make sure the Analysis Type is set to generic(ex:gProfiler)

4. Please select the following files by clicking on the respective (...) button and selecting the file in the Dialog:

GMT / hsapiens.NAME.gmt

Dataset 1 / Enrichments: sample_up.txt

5. Tune Parameters

P-value cut-off 1

Q-value cut-off 1

Overlap Coefficient cut-off 0.5

6. Click on the Build radio button at the bottom of the panel to create the Enrichment Map

7. In the menu bar, Go to View, and activate Show Graphics Details

8. In the control panel, go to Style, click on Label and select EM1_GS_DESCR in the Column dropdown. This will label nodes with names rather thsn GO IDs. The selected value may be EM2_GS_DESCR or other if you have more than one Enrichment Map open in Cytoscape

Enrichment map result

Cytoscape App Store
http://apps.cytoscape.org/

http://apps.cytoscape.org/

Never miss the Tutorial in each app page in the app store

Recap :
How to Decide ?
Micro-array Vs RNA-seq

Useful links in Metagenomics

Metagenomics analysis using Galaxy tutorial :

https://usegalaxy.org/u/james/p/exercise-metagenomics

Thank You

[email protected]

linked-in :
https://eg.linkedin.com/in/ali-kishk-997423a9

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Cytoscape in Plant Systems Biology

Data & Analytics

Transcript of Cytoscape in Plant Systems Biology