Gene annotation and pathway mapping in KEGG. Methods Mol Biol 2007 ; 396:71 - 91; http://dx.doi.org/ 10.1007/978-1-59745-515-2_6 ; PMID: 18025687Aoki-Kinoshita KF, Kanehisa M. Gene annotation and pathway mapping in KEGG. Methods Mol Biol. 2007; 396 :71–91. doi: 10.1007/978-1...
In this study with original KEGG pathways, none of the topology-based methods outperformed the gene set approach. Therefore, a second simulation study was performed on non-overlapping pathways created by unique gene IDs. Here, methods accounting for pathway topology reached higher accuracy than the ...
Functional annotations using COG, KEGG, CAZy, GO, CARD, and VFDB databases27,28,29,30 were also performed, leading to annotations for 66.9%, 46.1%, 1.7%, 17.2%, 0.01%, and 8.9% of the unigenes, respectively (Supplementary Fig. 5b, c and Supplementary Data 2.5). A total of 46,670...
scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data Article 26 September 2022 Mapping the functional network of human cancer through machine learning and pan-cancer proteogenomics Article 11 December 2024 Transformer for one stop interpre...
The analysis of GO enrichment results indicates that in the co expression module constructed by WGCNA, the genes of the Blue and Darkgrey modules play important roles in the growth of quinoa seedlings under different phosphorus treatment levels. Fig. 5 GO annotation (A, B), GO enrichment (C,...
Adrian Tivey, in International Journal for Parasitology, 2005 The next section of the feature page is ‘Gene Ontology Annotation’. The Gene Ontology (GO) (The Gene Ontology Consortium, 2000) consists of a trio of orthogonal controlled vocabularies; Biological Process, Cellular Component and ...
Then, with this DID (red), the annotation terms of interest (underlined) in different source files (OMIM, SMART, Pfam, GO Molecular Function, KEGG Pathway, BioCart Pathway, etc.) can be queried sequentially. Full size image DAVID gene concept: a novel single-linkage algorithm to agglomerate...
The assembly performed by the Cufflinks algorithm gives the researcher three possible approaches: reference annotation assembly (adjusted to transcriptome knowledge), reference annotation-based assembly (transcriptome-driven but allows the discovery of new entities), and without reference annotation assembly (...
GO annotation was used to study the DEGs function during tea embryogenesis (Fig. 2, Table S2). The main functions of the up-regulated DEGs in ES_PS were mainly enriched in photosynthesis, oxidoreductase activity, protein kinase activity, photosystem, integral component of membrane, thylakoid and ...
Organoids derived from stem cells have become an increasingly important tool for studying human development and modeling disease. However, methods are still needed to control and study spatiotemporal patterns of gene expression in organoids. Here we comb