I have proteomic data from Mass spectrometry and I cannot classify them by function to relate them with their effect on my cells.
The proteomic data is for a cellular extract. It has an antiproliferative effect on tumor cells, induces apoptosis, and induces cell cycle arrest.
I used Panther geneontology classification system and I found no relation by any of the afore mentioned functions. Please help me with another classification system or any advise.
Dear Zaynab El Gammal ,
Sometimes we do not find exactly the biological process or pathway that we think we should find, careful with these analyses. Proteomics and bioinformatics are difficult fields.
However, you can use other tools like:
https://david.ncifcrf.gov/
https://reactome.org/
http://amp.pharm.mssm.edu/Enrichr/
http://www.funrich.org/
Be very careful with the genes names this can cause confusion in Software.
Best,
Leite
You can enter the proteins identification code or GI number into EBI and search for the UniProtKB information. You can then alter the parameters in the output page to include GO terminology. You can then assemble common functional assignments or look up higher functional assignments for the GO terms. As the previous commentator has mentioned, be careful of creating a story before you look at the trends in the data. Also be careful of drawing conclusions from changes detected from low numbers of proteins.
Dear Zaynab,
I don't know exactly which kind of output that you already have for your proteomic analysis,
If you have already identified the peptide sequences of the Hypothetical proteins (HP) you can further run new analysis using bioinformatics tools to gain insight into their possible biological functions. This could be achieved using blastp and DELTA-BLAST from the National Center for Biotechnology Information (NCBI; http://blast.ncbi.nlm.nih.gov/Blast.cgi) to identify sequence similarity with known proteins. Afterward, conserved sites, domains and families already identified present in the HP could be studied using the Interproscan tool from the European Bioinformatics Institute (EBI; http://www.ebi.ac.uk/Tools/pfa/iprscan/).
Hope this helps,
All the best,
Younes,
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