Tutorial : the pipeline's modules?


Results summary

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1) After having clicked on results web-access button you will head on the main page of results [1]. You can download an Excel file with the results of each module.

Main page of results

ID resume

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1) The ID Mapping (ID Resume) module results are listed in a table [1]. this table provides proteins IDs, gene name, protein function, chromosite region, tissue specificity and subcellulare region. You can sort the table by using the dynamics table search area.

Main menu

Alignment

BlastP:

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1) Alignment results using BlastP Software:

Main page of results

GO - Gene Ontology

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1) Global informations about GO results module. You can find dynamics diagrams sort by GO functionnal group (Molecular Function, Biological Process and Cellular Component) and downloadable Excel files.

Main menu

2) Table of results for high-express GO (more than 1 annotation on the dataset). You can sort the table by Go function, Protein name or ID and Gene name, number of annotation or annotation frequency. Annotation frequency represent the percentage of protein annotate by the GO on the dataset. The covering frequency represent the percentage of gene product annotate by the GO on the dataset (against all gene products of the GO). Gene products are selected in function of the analysis species.

Main menu

3) This last table show each protein annotation.

Main menu

4) User can also visualize GO annotation as a tree chart network (with Cytoscape web API). Only linkable GO are selected and coloration represent ontology group (color darkening represent quantity of annotation made by the GO). GO a linked in function of their ancestor chart.

Main menu

Signal peptides

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1) Peptide prediction results using SignalP 4.1 software and GO terms related to secretion pathways are sort on a table. User can download an Excel file with each prediction results:

Signal peptide proteins

2) Potentially secreted proteins without signal peptide. Table resume the results of TargetP 1.0, subcellular location and GO terms related to secretion pathways. User can download an Excel file with each prediction results:

Without signal peptide proteins

Protein interactions (PPi)

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1) Results for Protein-protein interactions are resuming on a downloadable Excel file and a Cytoscape network:

Main page of results

2) Table of results about the PPi:

Table of results

Protein interactions (PPi) - Cytoscape web

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1) Network realyzed with Cytoscape web:

View of PPi using Cytoscape web

2) Protein-protein interactions legend (detection methods):

PPi legend

3) Cytoscape web settings:

Cytoscape web settings