scholarly journals 3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes

2004 ◽  
Vol 32 (90001) ◽  
pp. 245D-250 ◽  
Author(s):  
K. Fleming
Keyword(s):  
Functional Annotations ◽  
3D Genomics

Brief Survey of Biological Network Alignment and a Variant with Incorporation of Functional Annotations

2018 ◽  
Vol 14 (1) ◽  
pp. 4-10
Author(s):  
Fang Jing ◽  
Shao-Wu Zhang ◽  
Shihua Zhang
Keyword(s):  
Gene Ontology ◽  
Topological Structure ◽  
Metabolic Networks ◽  
Biological Network ◽  
Genomic Sequence ◽  
Network Alignment ◽  
Future Directions ◽  
Functional Annotations ◽  
Protein Protein Interaction ◽  
Ppi Networks

Background:Biological network alignment has been widely studied in the context of protein-protein interaction (PPI) networks, metabolic networks and others in bioinformatics. The topological structure of networks and genomic sequence are generally used by existing methods for achieving this task.Objective and Method:Here we briefly survey the methods generally used for this task and introduce a variant with incorporation of functional annotations based on similarity in Gene Ontology (GO). Making full use of GO information is beneficial to provide insights into precise biological network alignment.Results and Conclusion:We analyze the effect of incorporation of GO information to network alignment. Finally, we make a brief summary and discuss future directions about this topic.

scholarly journals Comparative genomics reveals new functional insights in uncultured MAST species

2021 ◽  
Author(s):  
Aurelie Labarre ◽  
David López-Escardó ◽  
Francisco Latorre ◽  
Guy Leonard ◽  
François Bucchini ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Genomic Data ◽  
Proton Pumps ◽  
Functional Annotations ◽  
The Core ◽  
Unicellular Eukaryotes ◽  
Microbial Eukaryotes ◽  
Core Energy ◽  
Marine Surface ◽  
Environmental Sequences

AbstractHeterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.

scholarly journals Entamoeba histolytica: Proteomics Bioinformatics Reveal Predictive Functions and Protein–Protein Interactions of Differentially Abundant Membrane and Cytosolic Proteins

Membranes ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 376
Author(s):  
Norhidayah Azmi ◽  
Nurulhasanah Othman
Keyword(s):  
Entamoeba Histolytica ◽  
Protein Interactions ◽  
Biological Process ◽  
Protein Protein Interactions ◽  
Differential Abundance ◽  
Cytosolic Proteins ◽  
Functional Annotations ◽  
Predictive Functions ◽  
Differentially Abundant Proteins ◽  
Abundance Proteins

Amoebiasis is caused by Entamoeba histolytica and ranked second for parasitic diseases causing death after malaria. E. histolytica membrane and cytosolic proteins play important roles in the pathogenesis. Our previous study had shown several cytosolic proteins were found in the membrane fraction. Therefore, this study aimed to quantify the differential abundance of membrane and cytosolic proteins in membrane versus cytosolic fractions and analyze their predicted functions and interaction. Previous LC-ESI-MS/MS data were analyzed by PERSEUS software for the differentially abundant proteins, then they were classified into their functional annotations and the protein networks were summarized using PantherDB and STRiNG, respectively. The results showed 24 (44.4%) out of the 54 proteins that increased in abundance were membrane proteins and 30 were cytosolic proteins. Meanwhile, 45 cytosolic proteins were found to decrease in abundance. Functional analysis showed differential abundance proteins involved in the molecular function, biological process, and cellular component with 18.88%, 33.04% and, 48.07%, respectively. The STRiNG server predicted that the decreased abundance proteins had more protein–protein network interactions compared to increased abundance proteins. Overall, this study has confirmed the presence of the differentially abundant membrane and cytosolic proteins and provided the predictive functions and interactions between them.

scholarly journals ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer’s disease

2021 ◽  
Author(s):  
Sijia Wu ◽  
Mengyuan Yang ◽  
Pora Kim ◽  
Xiaobo Zhou
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Rna Editing ◽  
Memory Loss ◽  
Brain Regions ◽  
Disease Stage ◽  
Mirna Regulation ◽  
Annotation Database ◽  
Functional Annotations ◽  
Genomic Landscape

Abstract A-to-I RNA editing, contributing to nearly 90% of all editing events in human, has been reported to involve in the pathogenesis of Alzheimer’s disease (AD) due to its roles in brain development and immune regulation, such as the deficient editing of GluA2 Q/R related to cell death and memory loss. Currently, there are urgent needs for the systematic annotations of A-to-I RNA editing events in AD. Here, we built ADeditome, the annotation database of A-to-I RNA editing in AD available at https://ccsm.uth.edu/ADeditome, aiming to provide a resource and reference for functional annotation of A-to-I RNA editing in AD to identify therapeutically targetable genes in an individual. We detected 1676 363 editing sites in 1524 samples across nine brain regions from ROSMAP, MayoRNAseq and MSBB. For these editing events, we performed multiple functional annotations including identification of specific and disease stage associated editing events and the influence of editing events on gene expression, protein recoding, alternative splicing and miRNA regulation for all the genes, especially for AD-related genes in order to explore the pathology of AD. Combing all the analysis results, we found 108 010 and 26 168 editing events which may promote or inhibit AD progression, respectively. We also found 5582 brain region-specific editing events with potentially dual roles in AD across different brain regions. ADeditome will be a unique resource for AD and drug research communities to identify therapeutically targetable editing events. Significance: ADeditome is the first comprehensive resource of the functional genomics of individual A-to-I RNA editing events in AD, which will be useful for many researchers in the fields of AD pathology, precision medicine, and therapeutic researches.

Storage, visualization, and navigation of 3D genomics data

Methods ◽  
2018 ◽  
Vol 142 ◽  
pp. 74-80 ◽  
Author(s):  
Jérôme Waldispühl ◽  
Eric Zhang ◽  
Alexander Butyaev ◽  
Elena Nazarova ◽  
Yan Cyr
Keyword(s):  
3D Genomics

scholarly journals Identification of Key Genes and miRNAs in Osteosarcoma Patients with Chemoresistance by Bioinformatics Analysis

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Binbin Xie ◽  
Yiran Li ◽  
Rongjie Zhao ◽  
Yuzi Xu ◽  
Yuhui Wu ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Regulation Of Transcription ◽  
Functional Annotations ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Search Tool ◽  
Poor Outcomes

Chemoresistance is a significant factor associated with poor outcomes of osteosarcoma patients. The present study aims to identify Chemoresistance-regulated gene signatures and microRNAs (miRNAs) in Gene Expression Omnibus (GEO) database. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) included positive regulation of transcription, DNA-templated, tryptophan metabolism, and the like. Then differentially expressed genes (DEGs) were uploaded to Search Tool for the Retrieval of Interacting Genes (STRING) to construct protein-protein interaction (PPI) networks, and 9 hub genes were screened, such as fucosyltransferase 3 (Lewis blood group) (FUT3) whose expression in chemoresistant samples was high, but with a better prognosis in osteosarcoma patients. Furthermore, the connection between DEGs and differentially expressed miRNAs (DEMs) was explored. GEO2R was utilized to screen out DEGs and DEMs. A total of 668 DEGs and 5 DEMs were extracted from GSE7437 and GSE30934 differentiating samples of poor and good chemotherapy reaction patients. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to perform GO and KEGG pathway enrichment analysis to identify potential pathways and functional annotations linked with osteosarcoma chemoresistance. The present study may provide a deeper understanding about regulatory genes of osteosarcoma chemoresistance and identify potential therapeutic targets for osteosarcoma.

Discovery and Characterization of Differentially Expressed Soybean MiRNAs and Their Targets During Soybean Mosaic Virus Infection Unveils Novel Insight Into Soybean-SMV Interaction

2021 ◽  
Author(s):  
Bowen Li ◽  
Adhimoolam Karthikeyan ◽  
Liqun Wang ◽  
Jinlong Yin ◽  
Tongtong Jin ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Target Genes ◽  
Soybean Mosaic Virus ◽  
Expression Patterns ◽  
Defense Responses ◽  
Pcr Analysis ◽  
Functional Annotations ◽  
Additional Information ◽  
Insight Into

Abstract Background: Soybean mosaic virus (SMV) is the most devastating pathogen of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21-24 nucleotides) and play important roles in regulating defense responses against pathogens. However, miRNA's response to SMV in soybean is not as well documented. Result: In this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1× Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi, and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs responded during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. Eventually, the expression patterns of several miRNAs validated by quantitative real-time PCR analysis are consistent with sequencing results. Conclusion: We have identified a large number of miRNAs and their target genes and also functional annotations. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.

scholarly journals CATH: expanding the horizons of structure-based functional annotations for genome sequences

2018 ◽  
Vol 47 (D1) ◽  
pp. D280-D284 ◽  
Author(s):  
Ian Sillitoe ◽  
Natalie Dawson ◽  
Tony E Lewis ◽  
Sayoni Das ◽  
Jonathan G Lees ◽  
...  
Keyword(s):  
Genome Sequences ◽  
Functional Annotations
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