Network Oriented multi-Omics Data Analysis and Integration
Run the full pipeline
Custom algorithms
Results download
Upload the Demo data
Demo
Provide the names of the conditions (phenotypes) analyzed and written in the xlsx sheets of the input omics files (DO NOT USE '_' for names!). Format example: Cool,Hot3,mkey
Conditions names
Provide the analyzed conditions (phenotypes) contrasts. They should be the names of the xlsx sheets. Format example: CoolvsHot3,mkeyvsCool,Hot3vsCool. Use 'vs' to write the contrasts
Conditions contrasts
Upload an archive containing at least one omics file. Each omics file needs to be an Excel table with the sheets containing a 'UniProt_ChEBI' column with Uniprot or ChEBI Ids in accordance with the documentation
Omics files archive
Browse...
Select the NetWalk framework restart probablity for weighted networks. This value will be used only if the input tables have a node weight column named 'Weight'
Weight factor
Download the input demo data
Demo
What is the directory index where your NOODAI analysis results are found? The index is provided after the input data is submitted for the analysis
Results directory index
Provide the names of the conditions (phenotypes) analyzed and written in the xlsx sheets of the input omics files (DO NOT USE '_' for names!). Format example: Cool,Hot3,mkey
Conditions names
Provide the analyzed conditions (phenotypes) contrasts. They should be the names of the xlsx sheets. Format example: CoolvsHot3,mkeyvsCool,Hot3vsCool. Use 'vs' to write the contrasts
Conditions contrasts
Provide the BioMart dataset used for the mapping of the protein Ids. For other organisms than the pre-loaded ones, provide the pre-formated interaction table! Check the documentation to see the full list of pre-loaded organisms
BioMart dataset
Provide the name of the splicing file in the archive. If you use splicing data, the contrast must be symmetric! Leave default for no DTU data
DTU file
Choose if you would like to use a pre-compiled interaction file, formated in accordance with the instructions. A default interaction file is available. For other organisms than the pre-loaded ones, upload a pre-compiled interaction file!
Use Pre-compiled Interaction file
No
Yes
Upload the BioGrid database file. Leave empty for default version 4.4.218
BioGrid database file
Browse...
Upload the STRING database file. Leave empty for default version 11.5
STRING database file
Browse...
Upload the IntAct database file. Leave empty for default release 245
IntAct database file
Browse...
Upload an archive containing at least one omics file. Each omics file needs to be an Excel table with the sheets containing a 'UniProt_ChEBI' column with Uniprot or ChEBI Ids in accordance with the documentation
Omics files archive
Browse...
Select the NetWalk framework restart probablity for weighted networks. This value will be used only if the input tables have a node weight column named 'Weight'
Weight factor
Upload the pre-formatted interaction database file. Leave empty for default
Interaction table file
Browse...
Upload an archive containing at least one omics file. Each omics file needs to be an Excel table with the sheets containing a 'UniProt_ChEBI' column with Uniprot or ChEBI Ids in accordance with the documentation
Omics files archive
Browse...
Select the NetWalk framework restart probablity for weighted networks. This value will be used only if the input tables have a node weight column named 'Weight'
Weight factor
Run the main network analysis algorithm extracting the top central nodes.
Submit
Provide the MONET analysis method options
MONET method
Provide the names of the databases against which the enrichment will be performed. Example: Reactome, Wikipathways
Pathways databases
Reactome
Wikipathways
BioCarta
PID
NetPath
HumanCyc
INOH
SMPDB
Provide the BioMart dataset used for the mapping of the protein Ids. For other organisms than the pre-loaded ones, provide the pre-formated interaction table! The available biomartID is only for humans. Alternatives: mmusculus_gene_ensembl, rnorvegicus_gene_ensembl, btaurus_gene_ensembl, dmelanogaster_gene_ensembl, drerio_gene_ensembl. See the documentation for the full list
BioMart dataset
Choose if you would like to use a pre-compiled interaction file, formated in accordance with the instructions. A default interaction file is available. For other organisms than the pre-loaded ones, upload a pre-compiled interaction file!
Use Pre-compiled Interaction file
No
Yes
Run the full multi-omics integrative analysis.
Submit
Upload interaction databases (Default ones are available)
Upload the BioGrid database file. Leave empty for default version 4.4.218
BioGrid database file
Browse...
Upload the STRING database file. Leave empty for default version 11.5
STRING database file
Browse...
Upload the IntAct database file. Leave empty for default release 245
IntAct database file
Browse...
Upload the pre-formatted interaction database file. Leave empty for default
Interaction table file
Browse...
If you would like to be notified when the analysis is completed, you can provide an email address.
Email address (Optional)
Provide the path where the network edges are saved.
Edge file path
Provide the MONET analysis method options
MONET method
Provide a temporary bin server. Leave empty for default
Temporary folder
Provide the monet executable path. Developer mode
MONET path
Run the MONET decomposition analysis.
Submit
Provide the names of the databases against which the enrichment is to be performed. Example: Reactome, Wikipathways
CPDB databases
Reactome
Wikipathways
BioCarta
PID
NetPath
HumanCyc
INOH
SMPDB
Provide the MONET background file. Leave empty for default
MONET background file
Browse...
Provide the CPDB database file. Leave empty for default
CPDB database file
Browse...
Extract the pathways associated with each network submodule.
Submit
Provide the edges' directory. Leave empty for default
Edge files directory
Provide the transcription factors dataset file. Leave empty for default
TF dataset
Browse...
Provide the network centralities file. Leave empty for default
Centralities file
Browse...
Provide the Kinome dataset file. Leave empty for default
Kinome Dataset
Browse...
Provide the file ending specific for a type of analysis. Default to 'Total'. Leave empty for default
File ending
Create the summary plots and report.
Submit
The directory where the NOODAI analysis results are found. The index is provided after the input data is submitted for the analysis
Results directory index
Save
Download the pre-compiled results for the Demo input data
Demo Results
