ProteINSIDE

Custom Analysis

1) General settings:

Job name: (30 caracters max)

IDs from the following species are analysed: BOVINE, HUMAN, RAT, MOUSE, GOAT and SHEEP

Select your species:

2) Input IDs:

Use a sample file:

Example of IDs that can be used: Q15848 or ADIPO_HUMAN or ADIPOQ or gi|62022275 (or login and use ProteCONVERT to get right IDs)

INPUT

OR

PASTE

File format (250 ko max / 4000 IDs max):

Microsoft Excel file (.xls or .xlsx)
Tablulation file (.tab or .txt)
DISABLE

OR

Paste your IDs (4000 IDs max):

Direct input

Input file tutorial : How to create my input file? Which file can I use?

3) Presets buttons:

You can use pre-set buttons and run the job OR select directly your own settings using the "4) Settings" section.

Select your species before using these buttons!

Options	Enable	Disable	Description
Basic Analysis Basic Analysis with PPI extension			Will activate same options as the Basic Analysis, and will activate a second search of PPi with protein outside of the dataset in the selected species.
Gene Ontology Complete Analysis			Will activate all options of the Functional Annotation module: electronic annotation and GOTree network.
Protein Interactions More interactions databases			Will activate all options of the Protein Interactions research. Will use interactions from databases of Protein-Protein and Smallmolecule-Protein interactions.
Full analysis All modules and all options			Will activate maximum settings and options for each module of ProteINSIDE.

4) Settings:

Functional annotation according to Gene Ontology:

1] Gene Ontology - software By selecting this option you activate the Functional Annotation using the GO module of ProteINSIDE (IEA evidence code are not selected)

2] Gene Ontology Tree - Tree network view for GO results (cytoscape web)

3] Use IEA evidence for GO Inferred from Electronic Annotation: Automatically-assigned GO for proteins

Prediction of signal peptides (powered with SignalP 4.1):

1] Signal peptide - software By selecting this option you activate the Prediction of signal peptides (SignalP 4.1) module of ProteINSIDE

2] Increase cleavage site sensitivity (D-cutoff 0.34) --> Informations (slightly higher false positive rate)

Protein-protein interactions (powered with Psicquic):

Psicquic webservice status: Service online ONLINE

1] Protein - protein interactions - software By selecting this option you activate the Protein-Protein Interactions module of ProteINSIDE

2] PPi software type:

Protein - protein interactions basic software (PPi within the dataset) - software
Protein - protein interactions custom software (PPi within and outside of the dataset) - software

Settings

Options

Number of interactions
by proteins

---> No more than interactions by protein

Active PPi with proteins
outside of the dataset

---> PPi research outside of the dataset:
Extend PPi research using protein outside of the dataset (see on FAQ)

Select the study species OR another species:
BlastP to select the most similar species

OR

Human Mouse Rat Goat Sheep Bovine

PPi databases

---> Select PPi databases among those proposed by Psicquic:
A] select all databases

OR

B] select the 3 most used databases (IntAct / UniProtKB / BioGrid)

OR

C] Select the databases depending on the interaction types:

Number of rows