amica: an interactive and user-friendly web-platform for the analysis of proteomics data

Autor(en)

Sebastian Didusch, Moritz Madern, Markus Hartl, Manuela Baccarini

Abstrakt

BACKGROUND: Quantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high throughput data analysis.

RESULTS: In order to facilitate this task for users with limited background knowledge, we have developed amica, a freely available open-source web-based software that accepts proteomic input files from different sources. amica provides quality control, differential expression, biological network and over-representation analysis on the basis of minimal user input. Scientists can use amica's query interface interactively to compare multiple conditions and rapidly identify enriched or depleted proteins. They can visualize their results using customized output graphics, and ultimately export the results in a tab-separated format that can be shared with collaborators. The code for the application, input data and documentation can be accessed online at github.com/tbaccata/amica and is also incorporated in the web application.

CONCLUSIONS: The strong emphasis on dynamic user interactions, the integration of various databases and the option to download processed data, facilitate the analysis of complex proteomic data for both first-time users and experienced bioinformaticians. A freely available version of amica is available at bioapps.maxperutzlabs.ac.at/app/amica .

Organisation(en)

Department für Mikrobiologie, Immunbiologie und Genetik, Department für Biochemie und Zellbiologie

Journal

BMC Genomics

Band

23

ISSN

1471-2164

DOI

https://doi.org/10.1186/s12864-022-09058-7

Publikationsdatum

12-2022

Peer-reviewed

Ja

ÖFOS 2012

106023 Molekularbiologie, 106052 Zellbiologie

Schlagwörter

ASJC Scopus Sachgebiete

Genetics, Biotechnology

Link zum Portal

https://ucrisportal.univie.ac.at/de/publications/amica-an-interactive-and-userfriendly-webplatform-for-the-analysis-of-proteomics-data(20370c49-743c-4aee-8dce-99dd99d5dbf6).html