Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Gene functional annotation and metabolic pathway analysis

TL Tingchun Li
HY Huaying Yang
YL Yan Lu
QD Qing Dong
GL Guihu Liu
FC Feng Chen
YZ Yingbing Zhou
request Request a Protocol
ask Ask a question
Favorite

The DEGs were annotated via alignment against and comparison with Pfam (http://pfam.xfam.org/), NCBI non-redundant (Nr) protein database (https://www.ncbi.nlm.nih.gov/refseq/), and SwissProt protein database (https://web.expasy.org/docs/swiss-prot_guideline.html). The GO terms including molecular function, biological process, and cellular component ontology were analyzed using Blast2GO program. Pathway assignments were conducted according to the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG, http://www.genome.jp/kegg). To map the target genes to metabolic pathways, all sequences of DEGs were uploaded to the Mercator v.3.6 (https://www.plabipd.de/portal/web/guest/mercator-sequence-annotation) to generate root map file, then it was imported to the Mapman software (V3.6.0 RC1) to obtain the map based on the transcriptome data (Kakumanu et al., 2012).

Copyright and License information:  ©2021 Li et al.
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

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.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A