Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Bioinformatics analysis of omics data

CC Claudia Di Carlo
BS Bebiana C. Sousa
MM Marcello Manfredi
JB Jessica Brandi
EP Elisa Dalla Pozza
EM Emilio Marengo
MP Marta Palmieri
ID Ilaria Dando
MW Michael J. O. Wakelam
AL Andrea F. Lopez-Clavijo
DC Daniela Cecconi
request Request a Protocol
ask Ask a question
Favorite

Bioinformatics analysis of proteomic data was performed as previously described52. Briefly, to characterize the function of proteins, gene ontology (GO) annotation, KEGG and Reactome pathways enrichment analyses were performed using STRING v.11.0 (http://string-db.org)53. The differentially expressed proteins were analysed for candidate functions and pathways enrichment, setting Homo sapiens as taxonomy, p < 0.05 and gene count > 2 as cut-off point.

Lipid profile levels obtained from the four PCSCs and P cells were loaded into an open access tool BioPAN, on LIPID MAPS Lipidomics Gateway (https://lipidmaps.org/biopan/)54. BioPAN provides Z-scores (Z > 1.645 at p < 0.05) using substrate and product lipid levels and integrate a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolic pathways.

Copyright and License information: The Author(s) ©2021
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A