SELPHI | Systematic Extrapolation of Linked Phospho-Interactions

Submit a Job

If you have questions about how to use this form, please see the documentation.

* indicates required fields. Note that either:
(1) a fasta database, OR
(2) a map of phosphosites and ID Map must be submitted.

Please do not submit files with spaces in their names.

Create a name for your job. Only use letters [a-z], numbers [0-9], and underscores [_]. Max 20 characters.

Jobname*

Species

Your input files must have the following columns: <br /> a) Protein or Proteins or Genes or Gene or Name or Names <br /> b) Peptide <br /> c) optional Intensity or Score columns. Any other columns will be considered as your phospho-data ratios.<br /><br />Supported data formats: .txt, .xls, xlsx

Input Data*

Upload file with the samples that you would like to merge. E.g.,:<br />Replicate1_M/L,Replicate2_M/L,Replicate3_M/L<br />Replicate1_H/L,Replicate2_H/L,Replicate3_H/L<br />Replicate1_H/M,Replicate2_H/M,Replicate3_H/M<br /><br />Supported data format: .txt (text file) only

Merge Samples File:

Select if your data has already been log transformed (default: not log transformed).

Log Transformation

Data has been log transformed

Select if you would like the motif over-representation analysis to be ran on your data (default: no motif analysis).

Analyze Motifs

Perform motif analysis

e.g. gi|8659574|ref|NP_006512.2| transcription factor E3 [Homo sapiens]_AApSDPLLSSVpSPAVSK TFE3_S547_S553<br /><br />Supported data formats: .txt, .xls, xlsx

Map of Phospho Sites*

Protein Matched UniprotID GeneName GeneID<br />
e.g. gi|8659574|ref|NP_006512.2| transcription factor E3 [Homo sapiens] TFE3_HUMAN TFE3 7030<br /><br />Supported data formats: .txt, .xls, xlsx

ID Map*

Database used to match your spectra to peptides/proteins.<br /><br />Supported data formats: .txt, .xls, xlsx

Fasta database*

Request clustering of phosphopeptides. Default: none

Clustering Method

Evidence to consider in STRING network overlap.

STRING evidence

Overall
Experimental
Database

GeneMania Integration

Physical interactions

Custom Settings

Fold change cutoff for considering peptide as ‘changed’ in the analysis (default: 3)

Ratio Cutoff

Kinase Cutoff

Correlation Cutoff

Correlation P-Value Cutoff

Minimum number of samples in which a peptide appears to consider it<br /> Can be between [1] and [Number of samples]

Minimum Samples

Indicate whether you want the maximum or average change value to be used when merging same peptides.

Merge Method

Method

Upload a file with a list of additional motifs to search for (see documentation for those that are already being searched).<br /><br />Data format: .txt (text file) only

Motif File

Minimum number of proteins included in a pathway to consider the pathway (default: 5)

Minimum Paths