Basic Analysis Custom Analysis Results access 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: BOVINE HUMAN RAT MOUSE GOAT SHEEP 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 AnalysisBasic 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 OntologyComplete Analysis Will activate all options of the Functional Annotation module: electronic annotation and GOTree network. Protein InteractionsMore interactions databases Will activate all options of the Protein Interactions research. Will use interactions from databases of Protein-Protein and Smallmolecule-Protein interactions. Full analysisAll 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 2] Gene Ontology Tree - Tree network view for GO results (cytoscape web) 3] Use IEA evidence for GO Prediction of signal peptides (powered with SignalP 4.1): 1] Signal peptide - software 2] Increase cleavage site sensitivity (D-cutoff 0.34) --> Informations (slightly higher false positive rate) Protein-protein interactions (powered with Psicquic): Psicquic webservice status: ONLINE 1] Protein - protein interactions - software 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 interactionsby proteins ---> No more than All 50 100 200 500 interactions by protein Active PPi with proteinsoutside 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 Default (5) 10 20 All Start the analysis You have to select an input file or paste your ID to be allow to run an analysis.