piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Behrouz Shamsaei; Szymon Chojnacki; Marcin Pilarczyk; Mehdi Najafabadi; Wen Niu; Chuming Chen; Karen Ross; Andrea Matlock; Jeremy Muhlich; Somchai Chutipongtanate; Jie Zheng; John Turner; Dušica Vidović; Jake Jaffe; Michael MacCoss; Cathy Wu; Ajay Pillai; Avi Ma'ayan; Stephan Schürer; Michal Kouril; Mario Medvedovic; Jarek Meller

doi:10.1093/nar/gkaa436

piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Nucleic Acids Res. 2020 Jul 2;48(W1):W85-W93. doi: 10.1093/nar/gkaa436.

Authors

Behrouz Shamsaei¹, Szymon Chojnacki¹, Marcin Pilarczyk¹, Mehdi Najafabadi¹, Wen Niu¹, Chuming Chen², Karen Ross³, Andrea Matlock⁴, Jeremy Muhlich⁵, Somchai Chutipongtanate^{6

7}, Jie Zheng⁸, John Turner⁹, Dušica Vidović⁹, Jake Jaffe¹⁰, Michael MacCoss¹¹, Cathy Wu^{2

3}, Ajay Pillai¹², Avi Ma'ayan¹³, Stephan Schürer⁹, Michal Kouril¹⁴, Mario Medvedovic^{1

15}, Jarek Meller^{1

14

16}

Affiliations

¹ Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA.
² Center for Bioinformatics & Computational Biology; University of Delaware, USA.
³ Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, USA.
⁴ Department of Biomedical Sciences, Cedars-Sinai Medical Center, USA.
⁵ Department of Systems Biology, Harvard Medical School, USA.
⁶ Department of Cancer Biology, University of Cincinnati College of Medicine, USA.
⁷ Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand.
⁸ Department of Genetics, University of Pennsylvania Perelman School of Medicine, USA.
⁹ Department of Pharmacology, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Center for Computational Science, University of Miami, Miami, USA.
¹⁰ Broad Institute of MIT and Harvard & Inzen Therapeutics, USA.
¹¹ Department of Genome Sciences, University of Washington, USA.
¹² Human Genome Research Institute, National Institutes of Health, Bethesda, USA.
¹³ Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, USA.
¹⁴ Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, USA.
¹⁵ Department of Biomedical Informatics, University of Cincinnati College of Medicine, USA.
¹⁶ Department of Electrical Engineering and Computer Science, University of Cincinnati, USA.

Abstract

Rapid progress in proteomics and large-scale profiling of biological systems at the protein level necessitates the continued development of efficient computational tools for the analysis and interpretation of proteomics data. Here, we present the piNET server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. The primary input for the server consists of a set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Several interconnected workflows can be used to generate: (i) interactive graphs and tables providing comprehensive annotation and mapping between peptides and proteins with PTM sites; (ii) high resolution and interactive visualization for enzyme-substrate networks, including kinases and their phospho-peptide targets; (iii) mapping and visualization of LINCS signature connectivity for chemical inhibitors or genetic knockdown of enzymes upstream of their target PTM sites. piNET has been built using a modular Spring-Boot JAVA platform as a fast, versatile and easy to use tool. The Apache Lucene indexing is used for fast mapping of peptides into UniProt entries for the human, mouse and other commonly used model organism proteomes. PTM-centric network analyses combine PhosphoSitePlus, iPTMnet and SIGNOR databases of validated enzyme-substrate relationships, for kinase networks augmented by DeepPhos predictions and sequence-based mapping of PhosphoSitePlus consensus motifs. Concordant LINCS signatures are mapped using iLINCS. For each workflow, a RESTful API counterpart can be used to generate the results programmatically in the json format. The server is available at http://pinet-server.org, and it is free and open to all users without login requirement.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
Computer Graphics
Enzymes / metabolism
Humans
Internet
Mice
Peptides / chemistry
Peptides / metabolism
Protein Processing, Post-Translational*
Proteins / chemistry
Proteins / metabolism
Proteomics / methods*
Software*
Workflow

Substances

Enzymes
Peptides
Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding