scholarly journals Identification and functional annotation of metabolism-associated lncRNAs and their related protein-coding genes in gastric cancer

2018 ◽  
Vol 6 (5) ◽  
pp. 728-738 ◽  
Author(s):  
Xiaoyan Mo ◽  
Tianwen Li ◽  
Yi Xie ◽  
Linwen Zhu ◽  
Bingxiu Xiao ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Functional Annotation ◽  
Related Protein ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 159 ◽  
Author(s):  
Stefanie Schindler ◽  
Karol Szafranski ◽  
Michael Hiller ◽  
Gul Ali ◽  
Saiprasad G Palusa ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Alternative Splicing ◽  
Related Protein ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 625
Author(s):  
Dongdong Bo ◽  
Xunping Jiang ◽  
Guiqiong Liu ◽  
Ruixue Hu ◽  
Yuqing Chong
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Testicular Development ◽  
Related Protein ◽  
Rna Seq ◽  
Down Regulation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Regulation Of Growth ◽  
Fresh Insight

Long intergenic non-coding RNAs (lincRNAs) regulate testicular development by acting on protein-coding genes. However, little is known about whether lincRNAs and protein-coding genes exhibit the same expression pattern in the same phase of postnatal testicular development in goats. Therefore, this study aimed to demonstrate the expression patterns and roles of lincRNAs during the postnatal development of the goat testis. Herein, the testes of Yiling goats with average ages of 0, 30, 60, 90, 120, 150, and 180 days postnatal (DP) were used for RNA-seq. In total, 20,269 lincRNAs were identified, including 16,931 novel lincRNAs. We identified seven time-specifically diverse lincRNA modules and six mRNA modules by weighted gene co-expression network analysis (WGCNA). Interestingly, the down-regulation of growth-related lincRNAs was nearly one month earlier than the up-regulation of spermatogenesis-related lincRNAs, while the down-regulation of growth-related protein-coding genes and the correspondent up-regulation of spermatogenesis-related protein-coding genes occurred at the same age. Then, potential lincRNA target genes were predicted. Moreover, the co-expression network of lincRNAs demonstrated that ENSCHIT00000000777, ENSCHIT00000002069, and ENSCHIT00000005076 were the key lincRNAs in the process of testis development. Our study discovered the divergent regulation patterns of lincRNA on spermatogenesis and testis growth, providing a fresh insight into age-biased changes in lincRNA expression in the goat testis.

scholarly journals Maize GO Annotation - Methods, Evaluation, and Review (maize-GAMER)

2017 ◽  
Author(s):  
Kokulapalan Wimalanathan ◽  
Iddo Friedberg ◽  
Carson M. Andorf ◽  
Carolyn J. Lawrence-Dill
Keyword(s):  
Gold Standard ◽  
Functional Annotation ◽  
Sequence Similarity ◽  
Protein Domain ◽  
High Coverage ◽  
Protein Coding ◽  
Go Annotation ◽  
Protein Coding Genes ◽  
Standard Set ◽  
Maize Protein

1SummaryWe created a new high-coverage, robust, and reproducible functional annotation of maize protein coding genes based on Gene Ontology (GO) term assignments. Whereas the existing Phytozome and Gramene maize GO annotation sets only cover 41% and 56% of maize protein coding genes, respectively, this study provides annotations for 100% of the genes. We also compared the quality of our newly-derived annotations with the existing Gramene and Phytozome functional annotation sets by comparing all three to a manually annotated gold standard set of 1,619 genes where annotations were primarily inferred from direct assay or mutant phenotype. Evaluations based on the gold standard indicate that our new annotation set is measurably more accurate than those from Phytozome and Gramene. To derive this new high-coverage, high-confidence annotation set we used sequence-similarity and protein-domain-presence methods as well as mixed-method pipelines that developed for the Critical Assessment of Function Annotation (CAFA) challenge. Our project to improve maize annotations is called maize-GAMER (GO Annotation Method, Evaluation, and Review) and the newly-derived annotations are accessible via MaizeGDB (http://download.maizegdb.org/maize-GAMER) and CyVerse (B73 RefGen_v3 5b+ at doi: doi.org/10.7946/P2S62P and B73 RefGen_v4 Zm00001d.2 at doi: doi.org/10.7946/P2M925).

scholarly journals Dysregulation of lncRNA in Helicobacter pylori-Infected Gastric Cancer Cells

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Leila Yousefi ◽  
Hamid Owaysee Osquee ◽  
Reza Ghotaslou ◽  
Mohammad Ahangarzadeh Rezaee ◽  
Tahereh Pirzadeh ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Helicobacter Pylori ◽  
Noncoding Rnas ◽  
Bacterial Virulence ◽  
Cancer Development ◽  
Biological Macromolecules ◽  
Gastric Cancer Cells ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
H Pylori

Helicobacter pylori (H. pylori) infection is the most common cause of gastric cancer (GC). This microorganism is genetically diverse; GC is caused by several genetic deregulations in addition to environmental factors and bacterial virulence factors. lncRNAs (long noncoding RNAs) are significant biological macromolecules in GC, have specific functions in diseases, and could be therapeutic targets. Altered lncRNAs can lead to the abnormal expression of adjacent protein-coding genes, which may be important in cancer development. Their mechanisms have not been well understood, so we are going to investigate the risk of GC in a population with both high lncRNA and H. pylori infection.

scholarly journals UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

2020 ◽  
Author(s):  
Alistair MacDougall ◽  
Vladimir Volynkin ◽  
Rabie Saidi ◽  
Diego Poggioli ◽  
Hermann Zellner ◽  
...  
Keyword(s):  
Experimental Evidence ◽  
Genome Sequencing ◽  
Functional Properties ◽  
Functional Annotation ◽  
Selection Criteria ◽  
Protein Family ◽  
Automatic Annotation ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. Results In response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. Availability and implementation UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot.org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi.ac.uk/uniprot-public/unifire.

scholarly journals Draft Genome Sequence of Curtobacterium sp. Strain ER1/6, an Endophytic Strain Isolated from Citrus sinensis with Potential To Be Used as a Biocontrol Agent

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Leandro Maza Garrido ◽  
João Marcelo Pereira Alves ◽  
Liliane Santana Oliveira ◽  
Arthur Gruber ◽  
Gabriel Padilla ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Functional Annotation ◽  
Citrus Sinensis ◽  
Biocontrol Agent ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Protein Coding Genes

Herein, we report a draft genome sequence of the endophytic Curtobacterium sp. strain ER1/6, isolated from a surface-sterilized Citrus sinensis branch, and it presented the capability to control phytopathogens. Functional annotation of the ~3.4-Mb genome revealed 3,100 protein-coding genes, with many products related to known ecological and biotechnological aspects of this bacterium.

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