scholarly journals Genome-wide profiling of 24 hr diel rhythmicity in the water flea, Daphnia pulex: network analysis reveals rhythmic gene expression and enhances functional gene annotation

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Samuel S. C. Rund ◽  
Boyoung Yoo ◽  
Camille Alam ◽  
Taryn Green ◽  
Melissa T. Stephens ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Gene Annotation ◽  
Daphnia Pulex ◽  
Functional Gene ◽  
Water Flea ◽  
Genome Wide ◽  
Rhythmic Gene ◽  
Functional Gene Annotation

scholarly journals Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779

PLoS Genetics ◽  
2012 ◽  
Vol 8 (11) ◽  
pp. e1003064 ◽  
Author(s):  
Astrid Vieler ◽  
Guangxi Wu ◽  
Chia-Hong Tsai ◽  
Blair Bullard ◽  
Adam J. Cornish ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Functional Gene ◽  
Nuclear Transformation ◽  
Nannochloropsis Oceanica ◽  
Functional Gene Annotation

scholarly journals Mining approximate frequent dense modules from multiple gene expression datasets

10.29007/d87q ◽  
2020 ◽  
Author(s):  
San Ha Seo ◽  
Saeed Salem
Keyword(s):  
Gene Expression ◽  
Gene Annotation ◽  
Expression Data ◽  
Frequent Subgraph Mining ◽  
Multiple Gene ◽  
Real Gene ◽  
Frequent Subgraph ◽  
Frequent Subgraphs ◽  
Coexpression Networks ◽  
Functional Gene Annotation

Large amount of gene expression data has been collected for various environmental and biological conditions. Extracting co-expression networks that are recurrent in multiple co-expression networks has been shown promising in functional gene annotation and biomarkers discovery. Frequent subgraph mining reports a large number of subnetworks. In this work, we propose to mine approximate dense frequent subgraphs. Our proposed approach reports representative frequent subgraphs that are also dense. Our experiments on real gene coexpression networks show that frequent subgraphs are biologically interesting as evidenced by the large percentage of biologically enriched frequent dense subgraphs.

scholarly journals Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants

2019 ◽  
Vol 35 (21) ◽  
pp. 4427-4429 ◽  
Author(s):  
Andrea Ghelfi ◽  
Kenta Shirasawa ◽  
Hideki Hirakawa ◽  
Sachiko Isobe
Keyword(s):  
Enzyme Commission ◽  
Gene Annotation ◽  
Sequence Similarity ◽  
Enzyme Commission Number ◽  
Functional Gene ◽  
Supplementary Information ◽  
Annotation System ◽  
Evidence Type ◽  
Similarity Searches ◽  
Functional Gene Annotation

Abstract Summary Hayai-Annotation Plants is a browser-based interface for an ultra-fast and accurate functional gene annotation system for plant species using R. The pipeline combines the sequence-similarity searches, using USEARCH against UniProtKB (taxonomy Embryophyta), with a functional annotation step. Hayai-Annotation Plants provides five layers of annotation: i) protein name; ii) gene ontology terms consisting of its three main domains (Biological Process, Molecular Function and Cellular Component); iii) enzyme commission number; iv) protein existence level; and v) evidence type. It implements a new algorithm that gives priority to protein existence level to propagate GO and EC information and annotated Arabidopsis thaliana representative peptide sequences (Araport11) within 5 min at the PC level. Availability and implementation The software is implemented in R and runs on Macintosh and Linux systems. It is freely available at https://github.com/kdri-genomics/Hayai-Annotation-Plants under the GPLv3 license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Correction: Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779

PLoS Genetics ◽  
2017 ◽  
Vol 13 (5) ◽  
pp. e1006802 ◽  
Author(s):  
Astrid Vieler ◽  
Guangxi Wu ◽  
Chia-Hong Tsai ◽  
Blair Bullard ◽  
Adam J. Cornish ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Functional Gene ◽  
Nuclear Transformation ◽  
Nannochloropsis Oceanica ◽  
Functional Gene Annotation

scholarly journals Gene network approach reveals co-expression patterns in nasal and bronchial epithelium

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Imkamp ◽  
Victor Bernal ◽  
Marco Grzegorzcyk ◽  
Peter Horvatovich ◽  
Cornelis J. Vermeulen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Gene Expression Profiling ◽  
Graphical Models ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Bronchial Epithelium ◽  
Differentially Expressed ◽  
Tobacco Exposure ◽  
Genome Wide

Abstract Nasal gene expression profiling is a new approach to investigate the airway epithelium as a biomarker to study the activity and treatment responses of obstructive pulmonary diseases. We investigated to what extent gene expression profiling of nasal brushings is similar to that of bronchial brushings. We performed genome wide gene expression profiling on matched nasal and bronchial epithelial brushes from 77 respiratory healthy individuals. To investigate differences and similarities among regulatory modules, network analysis was performed on correlated, differentially expressed and smoking-related genes using Gaussian Graphical Models. Between nasal and bronchial brushes, 619 genes were correlated and 1692 genes were differentially expressed (false discovery rate <0.05, |Fold-change|>2). Network analysis of correlated genes showed pro-inflammatory pathways to be similar between the two locations. Focusing on smoking-related genes, cytochrome-P450 pathway related genes were found to be similar, supporting the concept of a detoxifying response to tobacco exposure throughout the airways. In contrast, cilia-related pathways were decreased in nasal compared to bronchial brushes when focusing on differentially expressed genes. Collectively, while there are substantial differences in gene expression between nasal and bronchial brushes, we also found similarities, especially in the response to the external factors such as smoking.

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