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PhosPiR : an automa...
PhosPiR : an automated phosphoproteomic pipeline in R
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- Hong, Ye (författare)
- University of Turku
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- Flinkman, Dani (författare)
- University of Turku
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- Suomi, Tomi (författare)
- University of Turku
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- Pietilä, Sami (författare)
- University of Turku
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- James, Peter (författare)
- Lund University,Lunds universitet,Institutionen för immunteknologi,Institutioner vid LTH,Lunds Tekniska Högskola,Department of Immunotechnology,Departments at LTH,Faculty of Engineering, LTH
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- Coffey, Eleanor (författare)
- University of Turku
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- Elo, Laura L. (författare)
- University of Turku
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(creator_code:org_t)
- 2021-12-08
- 2022
- Engelska.
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Ingår i: Briefings in Bioinformatics. - : Oxford University Press (OUP). - 1467-5463 .- 1477-4054. ; 23:1
- Relaterad länk:
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http://dx.doi.org/10... (free)
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https://academic.oup...
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Large-scale phosphoproteome profiling using mass spectrometry (MS) provides functional insight that is crucial for disease biology and drug discovery. However, extracting biological understanding from these data is an arduous task requiring multiple analysis platforms that are not adapted for automated high-dimensional data analysis. Here, we introduce an integrated pipeline that combines several R packages to extract high-level biological understanding from large-scale phosphoproteomic data by seamless integration with existing databases and knowledge resources. In a single run, PhosPiR provides data clean-up, fast data overview, multiple statistical testing, differential expression analysis, phosphosite annotation and translation across species, multilevel enrichment analyses, proteome-wide kinase activity and substrate mapping and network hub analysis. Data output includes graphical formats such as heatmap, box-, volcano- and circos-plots. This resource is designed to assist proteome-wide data mining of pathophysiological mechanism without a need for programming knowledge.
Ämnesord
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
Nyckelord
- Bioinformatics
- Data visualization
- Phosphoproteomics
- Pipeline
- Proteomics
- Statistics
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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