PiNET

Annotate Peptides with PiNET.

Annotate PTM/Proteins with PiNET.

Annotate Genes with PiNET.

Enter peptides or use the list of
LINCS P100 peptides or try the list of LINCS GCP peptides 
{{motif}}
{{modification}}
{{abundance | limitTo:6}}

Notes

Peptide2Protein workflow can be used to map peptide moieties with post-translational modifications (PTMs) into proteins using a fast peptide to protein matching and PTM meta-data harmonization. Use the options below to select the reference proteome and other parameters.

While the PTMs2Modifires and Proteins2Pathways tabs can be used as stand-alone modules, using Peptides2Proteins tab will update the input for further analysis in these two tabs (PTMs2Modifires and Proteins2Pathways) based on the Peptide to PTM and Protein/Gene mappings.

For interactive submission, please limit the number of peptides to hundreds.

Please follow the convention in provided examples for the input syntax.

For Annotation of a List of Peptides:

http://eh3.uc.edu/pinet/peptideToProtein

For Annotation of a List of Peptides and Insert the Peptides with Values:

Please note the URL encodes as {:%7B, }:%7D, +:%2B, [:%5B, ]:%5D

http://eh3.uc.edu/pinet/peptideToProtein?list=IYQ[pY]IQSR[+42] 1.3,[aK]AYSFCGTVEY(UNIMOD:21)MAP -2.14

{{parsedPTMProtein}}

{{PTM}}  
{{abundance | limitTo:6}}

Notes

PTMs2Modifiers workflow can be used to map and visualize upstream modifying enzymes that target post-translational modification (PTM) sites in query proteins. These PTM sites are mapped automatically from peptide moieties with PTMs when using the Peptide2Protein workflow.

For interactive submission, please limit the number of PTM/Proteins to hundreds.

Please follow the convention in provided examples for the input syntax.

For Annotation of a List of PTM/Proteins:

http://eh3.uc.edu/pinet/ptmToModifier

For Annotation of a List of PTM/Proteins and Insert the PTM/Proteins:

In the following example the list of 'Q9Y463{[Y+80%5D@273} 2.11,Q13627{[Y+80]@321} 3.122,P51812{[S+80]@369} -1.92 is' sent for the query in the URL. Please note the URL encodes as {:%7B, }:%7D, +:%2B, [:%5B, ]:%5D

http://eh3.uc.edu/pinet/ptmToModifier?list=Q9Y463%7B%5BY%2B80%5D@273%7D 2.11,Q13627%7B%5BY%2B80%5D@321%7D 3.122,P51812%7B%5BS%2B80%5D@369%7D -1.92

 {{ctrl.numberOfAllValidGenes}} out of {{ctrl.numberOfAllInputGenes}} input genes are valid genes.

 Not valid genes are:
{{nonValid}} 
Gene name identification is case sensitive, Try other names of these genes or copy and paste the gene names again!
{{item.symbol}}
{{item.name}}
{{abundance| limitTo:6}}

Notes

Protein2Pathway workflow can be used to analyze and visualize protein (and thus gene) level data in terms of pathway enrichment analysis, pathway membership, upstream/downstream kinase network, and concordance with LINCS signatures.

For interactive submission, please limit the number of Genes to hundreds.

Please follow the convention in provided examples for the input syntax.

For Annotation of a List of Genes:

http://eh3.uc.edu/pinet/proteinToPathway

For Annotation of a List of Genes and Insert the Values:

In the following example the list of OCIAD1 0.11,NCOR2 -1.2,ZC3HC1 3.122,RPS6KA3 0.01,PDPK1 1.09,PDPK2P -0.92,HN1 1.76,BRAF -1.922,TP53 -2.542 is sent for the query in the URL.

http://eh3.uc.edu/pinet/proteinToPathway?list=OCIAD1 0.11,NCOR2 -1.2,ZC3HC1 3.122,RPS6KA3 0.01,PDPK1 1.09,PDPK2P -0.92,HN1 1.76,BRAF -1.922,TP53 -2.542