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I have a dataset containing the following kind of phosphorylation sites nomenclature:

aEDGAAPSPSSET(PhoS(Phos))Pk
aEDGAAPSPSSET(PhoS(Phos))Pkkk
eAEAAEPEQPEQPEQPAAEEPQAEEQSEAAGEk
eSGEGAEAEGATAEGAkDEAAAAAGGEGAAAPGEQAGGAGAEGAAGGEPR

Those with phosphorylation are in bold, and the other in plain text, all of them followed of a Fold Change and p-value for each condition comparison.

The final aim of these is to perform some kind of pathway analysis (open to suggestions)... I was going to start with webgestalt and do the phosphosites analysis. But their input ID has to be these:

Site ID annotation as the 15-mer sequence motif with the phosphosite in the middle or as the protein ID from Uniprot, Ensembl or RefSeq followed by the amino acid and its position (e.g. P12956_S51) is supported for the input for ORA and GSEA analysis. Liao,et al. WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs, Nucleic Acids Research, 2019, https://doi.org/10.1093/nar/gkz401

I would appreciate help to know how to convert my IDs to these ones and any recommendation to perform pathway analysis on this type of data.

Thank you!

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  • $\begingroup$ On the code block you used me lost the bold, also we don't see the fold change and p-value. To do this transformation you (and us) would need to know which protein are these sequences from. $\endgroup$ – llrs Feb 15 at 16:59

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