PubAg

Main content area

You searched for: Subject "gene ontology" Remove constraint Subject: "gene ontology"
Start Over

Search

1,352  Search Results

« Previous | 1 - 20 of 1,352 |
Number of results to display per page

Search Results

1. Curation and bioinformatic analysis of strabismus genes supports functional heterogeneity and proposes candidate genes with connections to RASopathies

Author:
Ye, Xin (Cynthia); van der Lee, Robin; Wasserman, Wyeth W.
Source:
Gene 2019 v.697 pp. 213-226
ISSN:
0378-1119
Subject:
gene ontology,   etc   ; bioinformatics; cerebellum; genes; loci; retina; tumor suppressor proteins;     Show all 7 Subjects
Abstract:
... Strabismus refers to the misalignment of the eyes and occurs in 2–4% of individuals. The low-resolution label “strabismus” covers a range of heterogeneous defects, which makes it challenging to unravel this condition. Consequently a coherent understanding of the causes is lacking. Here, we attempt to gain a better understanding of the underlying genetics by combining gene curation, diverse bioinfo ...
DOI:
10.1016/j.gene.2019.02.020

2. Too Many False Targets for MicroRNAs: Challenges and Pitfalls in Prediction of miRNA Targets and Their Gene Ontology in Model and Non‐model Organisms

Author:
Fridrich, Arie; Hazan, Yael; Moran, Yehu
Source:
BioEssays 2019 v.41 no.4 pp. e1800169
ISSN:
0265-9247
Subject:
gene ontology,   etc   ; RNA interference; bioinformatics; microRNA; models; prediction;     Show all 6 Subjects
Abstract:
... Short (“seed”) or extended base pairing between microRNAs (miRNAs) and their target RNAs enables post‐transcriptional silencing in many organisms. These interactions allow the computational prediction of potential targets. In model organisms, predicted targets are frequently validated experimentally; hence meaningful miRNA‐regulated processes are reported. However, in non‐models, these reports mos ...
DOI:
10.1002/bies.201800169

3. Cleavable hydrophobic derivatization strategy for enrichment and identification of phosphorylated lysine peptides

Author:
Hu, Yechen; Li, Yang; Gao, Hang; Jiang, Bo; Zhang, Xiaodan; Li, Xiao; Wu, Qiong; Liang, Zhen; Zhang, Lihua; Zhang, Yukui
Source:
Analytical and bioanalytical chemistry 2019 v.411 no.18 pp. 4159-4166
ISSN:
1618-2642
Subject:
gene ontology,   etc   ; Escherichia coli; biogenesis; biosynthesis; derivatization; hydrophobicity; lysine; peptides; proteins; proteome;     Show all 10 Subjects
Abstract:
... Because of structural flexibility and acid lability, the identification of phosphorylated lysine (pLys) peptides is a great challenge. We report here a cleavable hydrophobic derivatization (CHD) strategy for the enrichment and identification of pLys peptides. First, 2,5-dioxopyrrolidin-1-yl-3-(decyldisulfanyl)propanoate was synthesized to react with dephosphorylated lysine peptides, and then the d ...
DOI:
10.1007/s00216-019-01770-w

4. Tissue specific long non-coding RNAs are involved in aroma formation of black tea

Author:
Varshney, Deepti; Rawal, Hukam C.; Dubey, Himanshu; Bandyopadhyay, Tanoy; Bera, Biswajit; Kumar, P. Mohan; Singh, Nagendra Kumar; Mondal, Tapan Kumar
Source:
Industrial crops and products 2019 v.133 pp. 79-89
ISSN:
0926-6690
Subject:
gene ontology,   etc   ; black tea; genes; leaves; messenger RNA; microRNA; non-coding RNA; odors; tissues;     Show all 9 Subjects
Abstract:
... With the progress of sequencing technology coupled with in silico approaches, disclosure of long non-coding RNA (lncRNAs) from RNAseq data has become easy and reliable. Till today, no methodical investigation of lncRNAs and their regulatory roles in tea have been studied. In this study, using 170 RNAseq data (˜7157 million reads) of 11 harvestable tissues, 33,400 putative high certainty lncRNAs we ...
DOI:
10.1016/j.indcrop.2019.03.020

5. Transcriptome profile of rat genes in bone marrow-derived macrophages at different activation statuses by RNA-sequencing

Author:
Guo, Xue-Yan; Wang, Sai-Nan; Wu, Yan; Lin, Yu-Hong; Tang, Jie; Ding, Shu-Qin; Shen, Lin; Wang, Rui; Hu, Jian-Guo; Lü, He-Zuo
Source:
Genomics 2019 v.111 no.4 pp. 986-996
ISSN:
0888-7543
Subject:
gene ontology,   etc   ; gene expression; genes; macrophages; rats; sequence analysis; signal transduction; transcriptomics;     Show all 8 Subjects
Abstract:
... The underlying mechanisms of macrophage polarization have been detected by genome-wide transcriptome analysis in a variety of mammals. However, the transcriptome profile of rat genes in bone marrow-derived macrophages (BMM) at different activation statuses has not been reported. Therefore, we performed RNA-Sequencing to identify gene expression signatures of rat BMM polarized in vitro with differe ...
DOI:
10.1016/j.ygeno.2018.06.006

6. Protein–protein interaction network analysis of insecticide resistance molecular mechanism in Drosophila melanogaster

Author:
Zhang, GuiLu; Zhang, WenJun
Source:
Archives of insect biochemistry and physiology 2019 v.100 no.1 pp. e21523
ISSN:
0739-4462
Subject:
gene ontology,   etc   ; Drosophila melanogaster; bioinformatics; drugs; genes; insecticide resistance; insecticides; protein-protein interactions; proteins; topology;     Show all 10 Subjects
Abstract:
... The problem of resistance has not been solved fundamentally at present, because the development speed of new insecticides can not keep pace with the development speed of resistance, and the lack of understanding of molecular mechanism of resistance. Here we collected seed genes and their interacting proteins involved in insecticide resistance molecular mechanism in Drosophila melanogaster by liter ...
DOI:
10.1002/arch.21523

7. Classification of Widely and Rarely Expressed Genes with Recurrent Neural Network

Author:
Chen, Lei; Pan, XiaoYong; Zhang, Yu-Hang; Liu, Min; Huang, Tao; Cai, Yu-Dong
Source:
Computational and Structural Biotechnology Journal 2019 v.17 pp. 49-60
ISSN:
2001-0370
Subject:
gene ontology,   etc   ; biotechnology; data collection; gene expression; genes; humans; immune response; neoplasms; tissues;     Show all 9 Subjects
Abstract:
... A tissue-specific gene expression shapes the formation of tissues, while gene expression changes reflect the immune response of the human body to environmental stimulations or pressure, particularly in disease conditions, such as cancers. A few genes are commonly expressed across tissues or various cancers, while others are not. To investigate the functional differences between widely and rarely e ...
DOI:
10.1016/j.csbj.2018.12.002

8. Revealing Gene Function and Transcription Relationship by Reconstructing Gene-Level Chromatin Interaction

Author:
Liu, Li; Li, Qian-Zhong; Jin, Wen; Lv, Hao; Lin, Hao
Source:
Computational and Structural Biotechnology Journal 2019 v.17 pp. 195-205
ISSN:
2001-0370
Subject:
gene ontology,   etc   ; biotechnology; cell lines; chromatin; histones; humans; interphase; multigene family; sequence analysis; tissues; transcription (genetics);     Show all 11 Subjects
Abstract:
... Chromatin is hierarchically organized in human interphase nuclei. Dynamic chromatin interactions are thought to influence gene transcription and cell fate determination. A consensus concept is that genes may form transcription factories within nucleus by spatially interaction. However, it is still not well known whether the function-related genes co-locate in three-dimensional (3D) space for co-tr ...
DOI:
10.1016/j.csbj.2019.01.011

9. Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae)

Author:
Spalink, Daniel; Stoffel, Kevin; Walden, Genevieve K.; Hulse-Kemp, Amanda M.; Hill, Theresa A.; Van Deynze, Allen; Bohs, Lynn
Source:
Molecular phylogenetics and evolution 2018 v.126 pp. 293-302
ISSN:
1055-7903
Subject:
gene ontology,   etc   ; Capsicum; Lycianthes; genes; genomics; paraphyly; peppers; transcriptome; transcriptomics;     Show all 9 Subjects
Abstract:
... The integration of genomics and phylogenetics allows new insight into the structure of gene tree discordance, the relationships among gene position, gene history, and rate of evolution, as well as the correspondence of gene function, positive selection, and gene ontology enrichment across lineages. We explore these issues using the tribe Capsiceae (Solanaceae), which is comprised of the genera Lyc ...
DOI:
10.1016/j.ympev.2018.04.030

10. SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments

Author:
Hayes, Wayne B; Mamano, Nil
Source:
Bioinformatics 2018 v.34 no.8 pp. 1345-1352
ISSN:
1460-2059
Subject:
gene ontology,   etc   ; bioinformatics; protein-protein interactions; proteins; topology;     Show all 5 Subjects
Abstract:
... Gene Ontology (GO) terms are frequently used to score alignments between protein–protein interaction (PPI) networks. Methods exist to measure GO similarity between proteins in isolation, but proteins in a network alignment are not isolated: each pairing is dependent on every other via the alignment itself. Existing measures fail to take into account the frequency of GO terms across networks, inste ...
DOI:
10.1093/bioinformatics/btx716

11. Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families

Author:
Cesnik, Anthony J.; Shortreed, Michael R.; Schaffer, Leah V.; Knoener, Rachel A.; Frey, Brian L.; Scalf, Mark; Solntsev, Stefan K.; Dai, Yunxiang; Gasch, Audrey P.; Smith, Lloyd M.
Source:
Journal of proteome research 2018 v.17 no.1 pp. 568-578
ISSN:
1535-3907
Subject:
gene ontology,   etc   ; computer software; genes; proteome; salt stress; yeasts;     Show all 6 Subjects
Abstract:
... We present an open-source, interactive program named Proteoform Suite that uses proteoform mass and intensity measurements from complex biological samples to identify and quantify proteoforms. It constructs families of proteoforms derived from the same gene, assesses proteoform function using gene ontology (GO) analysis, and enables visualization of quantified proteoform families and their changes ...
DOI:
10.1021/acs.jproteome.7b00685

12. Near perfect protein multi-label classification with deep neural networks

Author:
Szalkai, Balázs; Grolmusz, Vince
Source:
Methods 2018 v.132 pp. 50-56
ISSN:
1046-2023
Subject:
gene ontology,   etc   ; amino acid sequences; artificial intelligence; neural networks; prediction;     Show all 5 Subjects
Abstract:
... Biological sequences can be considered as data items of high-, non-fixed dimensions, corresponding to the length of those sequences. The comparison and the classification of biological sequences in their relations to large databases are important areas of research today. Artificial neural networks (ANNs) have gained a well-deserved popularity among machine learning tools upon their recent successf ...
DOI:
10.1016/j.ymeth.2017.06.034

13. Interaction network analysis of YBX1 for identification of therapeutic targets in adenocarcinomas

Author:
Murugesan, Suriya Narayanan; Yadav, Birendra Singh; Maurya, Pramod Kumar; Chaudhary, Amit; Singh, Swati; Mani, Ashutosh
Source:
Journal of biosciences 2019 v.44 no.2 pp. 27
ISSN:
0250-5991
Subject:
gene ontology,   etc   ; adenocarcinoma; gene expression regulation; gene regulatory networks; genes; humans; lungs; sequence analysis; stomach; therapeutics; transcription (genetics);     Show all 11 Subjects
Abstract:
... Human Y-box binding protein-1 (YBX1) is a member of highly conserved cold-shock domain protein family, which is involved in transcriptional as well as translational regulation of many genes. Nuclear localization of YBX1 has been observed in various cancer types and it’s overexpression has been linked to adverse clinical outcome and poor therapy response, but no diagnostic or therapeutic correlatio ...
DOI:
10.1007/s12038-019-9848-8

14. mRNA and microRNA transcriptomics analyses in intermuscular bones of two carp species, rice flower carp (Cyprinus carpio var. Quanzhounensis) and Jian carp (Cyprinus carpio var. Jian)

Author:
Peng, Jinxia; Zeng, Digang; He, Pingping; Wei, Pinyuan; Hui, Wang; Wu, Tiejun; Zhuo, Xiaofei; Lin, Yong
Source:
Comparative biochemistry and physiology 2019 v.30 pp. 71-80
ISSN:
1744-117X
Subject:
gene ontology,   etc   ; Cyprinus carpio; bone mineralization; bones; carp; flowers; gene expression regulation; genes; messenger RNA; microRNA; rice; transcriptome; transcriptomics; China;     Show all 14 Subjects
Abstract:
... The rice flower carp (Cyprinus carpio var. Quanzhounensis) is a bony fish (superclass Osteichthyes), with very soft bones that is a significant feature unlike the other carp species. In this study, we analyzed the mRNA and microRNA (miRNA) transcriptomes in the intermuscular bones of rice flower carp and Jian carp (Cyprinus carpio var. Jian) (a typical member of common carp in China), using Illumi ...
DOI:
10.1016/j.cbd.2019.01.013

15. Acute effects of UVB radiation on the survival, growth, development, and reproduction of Daphniopsis tibetana Sars (Crustacea: Cladocera)

Author:
Wang, Meiru; Zhao, Wen; Wei, Jie; Wang, Shan; Xie, Xi
Source:
Environmental science and pollution research international 2019 v.26 no.11 pp. 10916-10925
ISSN:
0944-1344
Subject:
gene ontology,   etc   ; Cladocera; acute effects; evolutionary biology; gene expression regulation; genes; irradiation; lipids; population growth; reproduction; transcriptomics; ultraviolet radiation;     Show all 12 Subjects
Abstract:
... Daphniopsis tibetana Sars lives in elevation, usually with strong solar UV radiation. We speculate that UV may have an effect on the ecology and evolutionary biology of this species. However, the regulatory effect and mechanism of UV on D. tibetana have not been studied previously. Here, our results showed that UVB could act as a positive factor in the relative body lengths, reproductive parameter ...
DOI:
10.1007/s11356-019-04490-x

16. Comparative analysis of vertebral transcriptome in Japanese seabass (Lateolabrax japonicus) fed diets with varying phosphorus/calcium levels

Author:
Lu, Kang-Le; Rahimnejad, Samad; Ji, Zhong-Li; Zhang, Chun-Xiao; Wang, Ling; Song, Kai
Source:
Comparative biochemistry and physiology 2019 v.230 pp. 49-55
ISSN:
1095-6433
Subject:
gene ontology,   etc   ; Lateolabrax japonicus; aquaculture; aquatic environment; bone formation; calcium; gene expression regulation; genes; mineralization; osteoblasts; phosphorus; risk; transcriptome; vertebrae;     Show all 14 Subjects
Abstract:
... Aquaculture jeopardizes the aquatic environment by discharge of the most dietary phosphorus (P) into the water. Reducing the dietary P level is a common approach for decreasing the P discharge but it may result in increased risk of P deficiency leading to vertebral deformities. However, the molecular mechanism of vertebral deformities is poorly understood. We assessed vertebral transcriptome and c ...
DOI:
10.1016/j.cbpa.2018.12.010

17. Multiple Transcriptional Mechanisms Collectively Mediate Copper Resistance in Cupriavidus gilardii CR3

Author:
Huang, Ning; Mao, Juan; Zhao, Yan; Hu, Mingzhong; Wang, Xiaoyu
Source:
Environmental science & technology 2019 v.53 no.8 pp. 4609-4618
ISSN:
1520-5851
Subject:
gene ontology,   etc   ; Cupriavidus gilardii; bacteria; copper; gene expression regulation; genes; homeostasis; metabolism; prokaryotic cells; secretion; sulfur; transcription (genetics); transcriptome; transcriptomics;     Show all 14 Subjects
Abstract:
... Bacteria resist copper (Cu) stress by implementing several metabolic mechanisms. However, these mechanisms are not fully understood. We investigated the mechanism of Cu resistance in Cupriavidus gilardii CR3, a Cu-resistant bacterium with a fully sequenced, annotated genome. The growth of CR3 was inhibited by higher Cu concentrations (≥1.0 mM) but not by lower ones (≤0.5 mM). CR3 accumulated Cu in ...
DOI:
10.1021/acs.est.8b06787

18. A comprehensive profile and inter-individual variations analysis of the human normal amniotic fluid proteome

Author:
Liu, Xiang; Song, Yijun; Guo, Zhengguang; Sun, Wei; Liu, Juntao
Source:
Journal of proteomics 2019 v.192 pp. 1-9
ISSN:
1874-3919
Subject:
gene ontology,   etc   ; amnion; amniotic fluid; animal tissues; biomarkers; epithelial cells; excretion; extracellular matrix; humans; placenta; proteins; proteome; proteomics;     Show all 13 Subjects
Abstract:
... Amniotic fluid contains large amounts of proteins produced by amnion epithelial cells, fetal tissues, fetal excretions and placental tissues; thus, it is an important potential source of biomarkers for identifying fetal pathologies. In this study, a pooled AF sample from 7 healthy volunteers was used to provide a comprehensive profile of normal human AF proteome using immunoaffinity depletion of 1 ...
DOI:
10.1016/j.jprot.2018.04.023

19. Transcriptome profiling suggests roles of innate immunity and digestion metabolism in purplish Washington clam

Author:
Kim, Bo-Mi; Ahn, Do-Hwan; Kim, Hyejin; Lee, Jung Sick; Rhee, Jae-Sung; Park, Hyun
Source:
Genes & genomics 2019 v.41 no.2 pp. 183-191
ISSN:
1976-9571
Subject:
gene ontology,   etc   ; Crassostrea gigas; Saxidomus; biotransformation; clams; digestion; enzymes; food intake; genes; homeostasis; innate immunity; pharmacokinetics; transcriptome; transcriptomics;     Show all 14 Subjects
Abstract:
... The purplish Washington clam (Saxidomus purpuratus) in the family Veneridae is distributed widely along the intertidal zones of northeast Asia and is increasingly being utilized as a commercially important food resource. Bivalves maintain homeostasis by regulating their food intake and digestion, innate immunity, and biotransformation in a mollusk-specific organ, the digestive gland. To understand ...
DOI:
10.1007/s13258-018-0750-9

20. First de-novo transcriptome assembly, annotation and expression profiles of a freshwater snail (Semisulcospira coreana) fed with chlorella supplement

Author:
Lee, Sang Yoon; Lee, Sang-Min; Kim, Yi Kyung
Source:
Marine genomics 2019
ISSN:
1874-7787
Subject:
gene ontology,   etc   ; Chlorella; chlorophyllase; feeds; freshwater; gene expression; gene expression regulation; genes; ingestion; messenger RNA; physiological response; snails; transcriptome;     Show all 13 Subjects
Abstract:
... The aim of this study was to develop the transcriptome resource of Semisulcospira coreana that would support development of commercial feeds and physiological studies. We compared mRNA expression in S. coreana to determine gene transcripts that were differentially regulated responding two feeding conditions (with or without chlorella). A total of 13.1 G raw reads were obtained and assembled using ...
DOI:
10.1016/j.margen.2019.01.006