scholarly journals 'Gotta pick a megabase or two': In silico routes to gene regulation

2004 ◽  
Vol 3 (1) ◽  
pp. 12-14
Author(s):  
R. E. Hill
Keyword(s):  
Gene Regulation ◽  
In Silico

Identification of BAP1-associated MicroRNAs and Implications in Cancer Development

2019 ◽  
pp. 1-4
Author(s):  
Tikam Chand ◽  
Tikam Chand
Keyword(s):  
Gene Regulation ◽  
In Silico ◽  
Mirna Target ◽  
Target Prediction ◽  
Differential Regulation ◽  
Cancer Development ◽  
Mirna Target Prediction ◽  
Cancer Types ◽  
In Silico Tools

Having role in gene regulation and silencing, miRNAs have been implicated in development and progression of a number of diseases, including cancer. Herein, I present potential miRNAs associated with BAP1 gene identified using in-silico tools such as TargetScan and Exiqon miRNA Target Prediction. I identified fifteen highly conserved miRNA (hsa-miR-423-5p, hsa-miR-3184-5p, hsa-miR-4319, hsa-miR125b-5p, hsa-miR-125a-5p, hsa-miR-6893-3p, hsa-miR-200b-3p, hsa-miR-200c-3p, hsa-miR-505-3p.1, hsa-miR-429, hsa-miR-370-3p, hsa-miR-125a-5p, hsa-miR-141-3p, hsa-miR-200a-3p, and hsa-miR-429) associated with BAP1 gene. We also predicted the differential regulation of these twelve miRNAs in different cancer types.

Reverse Engineering of Gene Regulation Networks with an Application to the DREAM4 in silico Network Challenge

2011 ◽  
pp. 461-477 ◽  
Author(s):  
Hyonho Chun ◽  
Jia Kang ◽  
Xianghua Zhang ◽  
Minghua Deng ◽  
Haisu Ma ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Reverse Engineering ◽  
In Silico ◽  
Gene Regulation Networks

In Silico Analysis of miRNA-Mediated Gene Regulation in OCA and OA Genes

2014 ◽  
Vol 70 (3) ◽  
pp. 1923-1932 ◽  
Author(s):  
Balu Kamaraj ◽  
Chandrasekhar Gopalakrishnan ◽  
Rituraj Purohit
Keyword(s):  
Gene Regulation ◽  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis

Sa1672 - Apc Gene Regulation by Mir-135A and Mir-135B in Sporadic Colorectal Cancer: In Silico Approach and Expression Analysis

2018 ◽  
Vol 154 (6) ◽  
pp. S-349
Author(s):  
Mumtaz Anwar ◽  
Rakesh Kochhar ◽  
Deepak Kaul ◽  
Alka Bhatia ◽  
Safrun Mahmood
Keyword(s):  
Colorectal Cancer ◽  
Gene Regulation ◽  
Expression Analysis ◽  
In Silico ◽  
Apc Gene ◽  
Sporadic Colorectal Cancer

scholarly journals In silico analysis of promoter region and regulatory elements of mitogenome co-expressed trn gene clusters encoding for bio-pesticide in entomopathogenic fungus, Metarhizium anisopliae: strain ME1

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Getachew Bantihun ◽  
Mulugeta Kebede
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Entomopathogenic Fungi ◽  
Metarhizium Anisopliae ◽  
In Silico ◽  
Promoter Region ◽  
Gene Clusters ◽  
Regulatory Elements ◽  
Predictive Score ◽  
Promoter Regions

Abstract Background Pest control strategies almost entirely rely on chemical insecticides, which cause environmental problems such as biosphere deterioration and emergence of resistant pests. Bio-pesticide is an alternative approach, which uses organisms such as entomopathogenic fungi, Metarhizium anisopliae, to control pests. Screening such potential organism at a molecular level and understanding their gene regulation mechanism is an important approach to reduce emergence of pesticide resistance and worsening of the biosphere. Understanding promoter regions which play a pivotal role in gene regulation is crucial. In particular, identification of the promoter regions in M. anisopliae Strain ME1 remains poorly understood. To our knowledge, the mitogenome trn gene clusters of M. anisopliae Strain ME1 were not characterized. Here, we used machine learning approach to identify and characterize the promoter regions, regulatory elements, and CpG island densities of 15 protein coding genes of entomopathogenic fungi, M. anisolpliae Strain ME1. Results The current analysis revealed multiple transcription start sites (TSS) for all utilized sequences, except for promoter region genes of Pro-cob and Pro-nad5. With reference to the start codon (ATG), 85.3% of TSS was located above – 500 bp. Based on the standard predictive score at cut off value of 0.8a, the current study revealed 54.7% of predictive score greater than or equal from 0.9 promoter prediction score. Expectation maximization algorithm output identified five candidate motifs. Nonetheless, of all candidate motifs, MtrnI was revealed as the common promoter region motif with a value of 76.9% both in terms of size of binding sites and with an E value of 9.1E−054. Accordingly, we perceived that MtrnI serve as the binding site for tryptophan cluster with P value 0.0044 and C4 type zinc fingers functions as the binding site to regulate gene expression of M. anisopliae Strain ME1. The analysis revealed that mitogenome trn gene clusters of M. anisopliae Strain ME1 showed homologues evolutionary ancestor supported with a bootstrap value of 100%. Conclusion Identified common candidate motifs and binding transcription factors through in silico approach are likely expected to contribute for better understanding of gene expression and strain improvement of M. anisopliae Strain ME1 for its bio-pesticides role.

scholarly journals An in silico analysis of robust but fragile gene regulation links enhancer length to robustness

2019 ◽  
Author(s):  
Kenneth A Barr ◽  
John Reinitz ◽  
Ovidiu Radulescu
Keyword(s):  
Gene Regulation ◽  
In Silico ◽  
In Silico Analysis ◽  
Mathematical Concept ◽  
Sequence Length ◽  
Local Concentration ◽  
Quantitative Evidence ◽  
Regulatory Systems ◽  
Genetic Sequences ◽  
Gene Regulatory

1AbstractOrganisms must ensure that expression of genes is directed to the appropriate tissues at the correct times, while simultaneously ensuring that these gene regulatory systems are robust to perturbation. This idea is captured by a mathematical concept called r-robustness, which says that a system is robust to a perturbation in up to r - 1 randomly chosen parameters. In this work we use this idea to investigate the robustness of gene regulation using a sequence level model of the Drosophila melanogaster gene even-skipped. We find that gene regulation can be remarkably sensitive to changes in transcription factor concentrations at the boundaries of expression features, while it is robust to perturbation elsewhere. We also find that the length of sequence used to control an expression feature correlates negatively with the number of nucleotides that are sensitive to mutation in both natural and in silico predicted enhancers. In all cases, the exact degree of robustness obtained is dependent not only on DNA sequence, but also on the local concentration of regulatory factors. By analyzing both natural and synthetic sequences, we provide strong quantitative evidence that increased sequence length makes gene regulatory systems more robust to genetic perturbation.2Author SummaryRobustness assures that organisms can survive when faced with unpredictable environments or genetic mutations. In this work, we characterize the robustness of gene regulation using an experimentally validated model of the regulation of the Drosophila gene even-skipped. We use a mathematically precise definition of robustness that allows us to make quantitative comparisons of robustness between different genetic sequences or between different nuclei. From this analysis, we found that genetic sequences that were not previously known to be important for gene regulation reduce sensitivity to genetic perturbation. In contrast, we found that gene regulation can be very sensitive to the levels of regulators. This extreme sensitivity was only observed at the boundaries of expression features, where switch-like behavior is desirable. This highlights the importance of considering context when assessing robustness.

scholarly journals The role of mobile genetic elements in evolution of cyanobacteria

2011 ◽  
Vol 9 (4) ◽  
pp. 52-62
Author(s):  
Lidia E Mikheeva ◽  
Elena A Karbysheva ◽  
Sergey V Shestakov
Keyword(s):  
Gene Regulation ◽  
Significant Role ◽  
In Silico ◽  
In Silico Analysis ◽  
Whole Genome ◽  
Number Of Genes ◽  
Genes Encoding ◽  
Adaptation Processes ◽  
Silico Analysis

Possible pathways of cyanobacterial evolution are discussed on the basis of in silico analysis of fully sequenced genomes of 45 species/strains of cyanobacteria. The information on quantity and functions of different mobile elements (IS, MITE elements and group II introns) was reviewed. Positive correlation between whole genome sizes and number of genes, encoding transposases has been revealed. It is suggested that transpositions play significant role in genome rearrangements taking part in gene regulation and adaptation processes determining the directions of microevolution processes in cyanobacterial populations.

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