scholarly journals YQFC: a web tool to compare quantitative biological features between two yeast gene lists

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Wei-Sheng Wu ◽  
Lai-Ji Wang ◽  
Han-Chen Yen ◽  
Yan-Yuan Tseng
Keyword(s):  
High Throughput ◽  
Half Life ◽  
Enrichment Analysis ◽  
Biological Research ◽  
Translational Efficiency ◽  
Yeast Gene ◽  
Mrna Isoforms ◽  
Omics Technologies ◽  
Quantitative Feature ◽  
Analysis Tools

Abstract Nowadays high-throughput omics technologies are routinely used in biological research. From the omics data, researchers can easily get two gene lists (e.g. stress-induced genes vs. stress-repressed genes) related to their biological question. The next step would be to apply enrichment analysis tools to identify distinct functional/regulatory features between these two gene lists for further investigation. Although various enrichment analysis tools are already available, two challenges remain to be addressed. First, most existing tools are designed to analyze only one gene list, so they cannot directly compare two gene lists. Second, almost all existing tools focus on identifying the enriched qualitative features (e.g. gene ontology [GO] terms, pathways, domains, etc.). Many quantitative features (e.g. number of mRNA isoforms of a gene, mRNA half-life, protein half-life, transcriptional plasticity, translational efficiency, etc.) are available in the yeast, but no existing tools provide analyses on these quantitative features. To address these two challenges, here we present Yeast Quantitative Features Comparator (YQFC) that can directly compare various quantitative features between two yeast gene lists. In YQFC, we comprehensively collected and processed 85 quantitative features from the yeast literature and yeast databases. For each quantitative feature, YQFC provides three statistical tests (t-test, U test and KS test) to test whether this quantitative feature is statistically different between the two input yeast gene lists. The distinct quantitative features identified by YQFC may help researchers to study the underlying molecular mechanisms that differentiate the two input yeast gene lists. We believe that YQFC is a useful tool to expedite the biological research that uses high-throughput omics technologies. Database URL http://cosbi2.ee.ncku.edu.tw/YQFC/

scholarly journals A Review on Bioinformatics Enrichment Analysis Tools Towards Functional Analysis of High Throughput Gene Set Data

2015 ◽  
Vol 12 (1) ◽  
pp. 14-27 ◽  
Author(s):  
Lu Shi Jing ◽  
Farah Fathiah Muzaffar Shah ◽  
Mohd Saberi Mohamad ◽  
Kohbalan Moorthy ◽  
Safaai Deris ◽  
...  
Keyword(s):  
Functional Analysis ◽  
High Throughput ◽  
Enrichment Analysis ◽  
Gene Set ◽  
Analysis Tools

Next-Generation Sequencing: An Emerging Tool for Drug Designing

2019 ◽  
Vol 25 (31) ◽  
pp. 3350-3357 ◽  
Author(s):  
Pooja Tripathi ◽  
Jyotsna Singh ◽  
Jonathan A. Lal ◽  
Vijay Tripathi
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Massively Parallel Sequencing ◽  
Genomic Research ◽  
Biological Research ◽  
Next Generation ◽  
Human Welfare ◽  
Drug Designing ◽  
Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

scholarly journals FAN-C: A Feature-rich Framework for the Analysis and Visualisation of C data

2020 ◽  
Author(s):  
Kai Kruse ◽  
Clemens B. Hug ◽  
Juan M. Vaquerizas
Keyword(s):  
High Throughput ◽  
Matrix Analysis ◽  
Set Covering ◽  
Command Line ◽  
Chromosome Conformation ◽  
C Storage ◽  
Data Formats ◽  
Analysis Tools ◽  
Command Line Tool ◽  
Broad Feature

Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C and its derivatives, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool and powerful Python API with a broad feature set covering matrix generation, analysis, and visualisation for C-like data (https://github.com/vaquerizaslab/fanc). Due to its comprehensiveness and compatibility with the most prevalent Hi-C storage formats, FAN-C can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.

scholarly journals T-Cell Intracellular Antigens and Hu Antigen R Antagonistically Modulate Mitochondrial Activity and Dynamics by Regulating Optic Atrophy 1 Gene Expression

2017 ◽  
Vol 37 (17) ◽  
Author(s):  
Isabel Carrascoso ◽  
José Alcalde ◽  
Carmen Sánchez-Jiménez ◽  
Paloma González-Sánchez ◽  
José M. Izquierdo
Keyword(s):  
T Cell ◽  
Optic Atrophy ◽  
Morphological Changes ◽  
Dynamic Network ◽  
Mitochondrial Activity ◽  
Translational Efficiency ◽  
Mrna Isoforms ◽  
Mitochondrial Dynamic ◽  
Mitochondrial Dna Damage ◽  
Hu Antigen R

ABSTRACT Mitochondria undergo frequent morphological changes to control their function. We show here that T-cell intracellular antigens (TIA1b/TIARb) and Hu antigen R (HuR) have antagonistic roles in mitochondrial function by modulating the expression of mitochondrial shaping proteins. Expression of TIA1b/TIARb alters the mitochondrial dynamic network by enhancing fission and clustering, which is accompanied by a decrease in respiration. In contrast, HuR expression promotes fusion and cristae remodeling and increases respiratory activity. Mechanistically, TIA proteins downregulate the expression of optic atrophy 1 (OPA1) protein via switching of the splicing patterns of OPA1 to facilitate the production of OPA1 variant 5 (OPA1v5). Conversely, HuR enhances the expression of OPA1 mRNA isoforms through increasing steady-state levels and targeting translational efficiency at the 3′ untranslated region. Knockdown of TIA1/TIAR or HuR partially reversed the expression profile of OPA1, whereas knockdown of OPA1 or overexpression of OPA1v5 provoked mitochondrial clustering. Middle-term expression of TIA1b/TIARb triggers reactive oxygen species production and mitochondrial DNA damage, which is accompanied by mitophagy, autophagy, and apoptosis. In contrast, HuR expression promotes mitochondrion-dependent cell proliferation. Collectively, these results provide molecular insights into the antagonistic functions of TIA1b/TIARb and HuR in mitochondrial activity dynamics and suggest that their balance might contribute to mitochondrial physiopathology.

scholarly journals Bioinformatics in otolaryngology research. Part one: concepts in DNA sequencing and gene expression analysis

2014 ◽  
Vol 128 (10) ◽  
pp. 848-858 ◽  
Author(s):  
T J Ow ◽  
K Upadhyay ◽  
T J Belbin ◽  
M B Prystowsky ◽  
H Ostrer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Data Storage ◽  
Expression Analysis ◽  
High Throughput ◽  
Gene Expression Analysis ◽  
Biological Data ◽  
Biological Research ◽  
Nucleotide Sequencing ◽  
New Era ◽  
Crucial Component

AbstractBackground:Advances in high-throughput molecular biology, genomics and epigenetics, coupled with exponential increases in computing power and data storage, have led to a new era in biological research and information. Bioinformatics, the discipline devoted to storing, analysing and interpreting large volumes of biological data, has become a crucial component of modern biomedical research. Research in otolaryngology has evolved along with these advances.Objectives:This review highlights several modern high-throughput research methods, and focuses on the bioinformatics principles necessary to carry out such studies. Several examples from recent literature pertinent to otolaryngology are provided. The review is divided into two parts; this first part discusses the bioinformatics approaches applied in nucleotide sequencing and gene expression analysis.Conclusion:This paper demonstrates how high-throughput nucleotide sequencing and transcriptomics are changing biology and medicine, and describes how these changes are affecting otorhinolaryngology. Sound bioinformatics approaches are required to obtain useful information from the vast new sources of data.

Advancements in High-Throughput Omics-Technologies for Understanding the Biology of Neglected and Underutilized Crops

2021 ◽  
pp. 203-236
Author(s):  
Ashish Kumar Choudhary ◽  
Riyazuddin Riyazuddin ◽  
Arun Kumar Maurya ◽  
Ravi Gupta
Keyword(s):  
High Throughput ◽  
Underutilized Crops ◽  
Omics Technologies

scholarly journals High-throughput screening and chemotype-enrichment analysis of ToxCast phase II chemicals evaluated for human sodium-iodide symporter (NIS) inhibition

2019 ◽  
Vol 126 ◽  
pp. 377-386 ◽  
Author(s):  
Jun Wang ◽  
Daniel R. Hallinger ◽  
Ashley S. Murr ◽  
Angela R. Buckalew ◽  
Ryan R. Lougee ◽  
...  
Keyword(s):  
Phase Ii ◽  
High Throughput ◽  
High Throughput Screening ◽  
Sodium Iodide ◽  
Enrichment Analysis ◽  
Sodium Iodide Symporter

scholarly journals High-throughput quantitative microscopy-based half-life measurements of intravenously injected agents

2020 ◽  
Vol 117 (7) ◽  
pp. 3502-3508
Author(s):  
Laura G. Bracaglia ◽  
Alexandra S. Piotrowski-Daspit ◽  
Chun-Yu Lin ◽  
Zoe M. Moscato ◽  
Yongheng Wang ◽  
...  
Keyword(s):  
High Throughput ◽  
Blood Concentration ◽  
Half Life ◽  
Polymeric Nanoparticles ◽  
Quantitative Microscopy ◽  
Preclinical Development ◽  
Accurate Analysis ◽  
Multiple Samples ◽  
Improved Accuracy ◽  
Surface Chemistries

Accurate analysis of blood concentration and circulation half-life is an important consideration for any intravenously administered agent in preclinical development or for therapeutic application. However, the currently available tools to measure these parameters are laborious, expensive, and inefficient for handling multiple samples from complex multivariable experiments. Here we describe a robust high-throughput quantitative microscopy-based method to measure the blood concentration and circulation half-life of any fluorescently labeled agent using only a small (2 µL) amount of blood volume, enabling additional end-point measurements to be assessed in the same subject. To validate this method, we demonstrate its use to measure the circulation half-life in mice of two types of fluorescently labeled polymeric nanoparticles of different sizes and surface chemistries and of a much smaller fluorescently labeled monoclonal antibody. Furthermore, we demonstrate the improved accuracy of this method compared to previously described methods.

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