iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations

We consider the three-dimensional gene regulatory network (GRN in short). This model consists of ordinary differential equations of a special kind, where the nonlinearity is represented by a sigmoidal function and the linear part is present also. The evolution of GRN is described by the solution vector X(t), depending on time. We describe the changes that system undergoes if the entries of the regulatory matrix are perturbed in some way.

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Faculty Opinions recommendation of Genomic analysis of regulatory network dynamics reveals large topological changes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1022077.250670 ◽

2004 ◽

Author(s):

Philip Benfey

Keyword(s):

Regulatory Network ◽

Network Dynamics ◽

Genomic Analysis ◽

Topological Changes

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Genomic analysis of xCT-regulatory network in KSHV + primary effusion lymphomas

Genomics Data ◽

10.1016/j.gdata.2016.02.011 ◽

2016 ◽

Vol 8 ◽

pp. 16-17

Author(s):

Zhiqiang Qin ◽

Yueyu Cao ◽

Lu Dai

Keyword(s):

Regulatory Network ◽

Genomic Analysis ◽

Primary Effusion Lymphomas

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Functional Genomic Analysis of the let-7 Regulatory Network in Caenorhabditis elegans

PLoS Genetics ◽

10.1371/journal.pgen.1003353 ◽

2013 ◽

Vol 9 (3) ◽

pp. e1003353 ◽

Cited By ~ 29

Author(s):

Shaun E. Hunter ◽

Emily F. Finnegan ◽

Dimitrios G. Zisoulis ◽

Michael T. Lovci ◽

Katya V. Melnik-Martinez ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Regulatory Network ◽

Genomic Analysis ◽

Functional Genomic ◽

Functional Genomic Analysis

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Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

Molecular Systems Biology ◽

10.1038/msb.2009.52 ◽

2009 ◽

Vol 5 (1) ◽

pp. 294 ◽

Cited By ~ 104

Author(s):

Raja Jothi ◽

S Balaji ◽

Arthur Wuster ◽

Joshua A Grochow ◽

Jörg Gsponer ◽

...

Keyword(s):

Transcription Factor ◽

Regulatory Network ◽

Network Architecture ◽

Genomic Analysis

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Spatial organization of the transcriptional regulatory network of Saccharomyces cerevisiae

10.1101/509224 ◽

2019 ◽

Author(s):

Dong-Qing Sun ◽

Liu Tian ◽

Bin-Guang Ma

Keyword(s):

Saccharomyces Cerevisiae ◽

Regulatory Network ◽

Spatial Organization ◽

Target Genes ◽

Transcriptional Regulatory Network ◽

3D Structure ◽

Three Dimensional ◽

3D Genome ◽

Transcriptional Regulatory ◽

Four Levels

AbstractTranscriptional regulatory network (TRN) is a directed complex network composed of all regulatory interactions between transcription factors and corresponding target genes. Recently, the three-dimensional (3D) genomics studies have shown that the 3D structure of the genome makes a difference to the regulation of gene transcription, which provides us with a novel perspective. In this study, we constructed the TRN of the budding yeast Saccharomyces cerevisiae and placed it in the context of 3D genome model. We analyzed the spatial organization of the yeast TRN on four levels: global feature, central nodes, hierarchical structure and network motifs. Our results suggested that the TRN of S. cerevisiae presents an optimized structure in space to adapt to functional requirement.

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Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13

Viruses ◽

10.3390/v14010006 ◽

2021 ◽

Vol 14 (1) ◽

pp. 6

Author(s):

Olga Pacios ◽

Laura Fernández-García ◽

Inés Bleriot ◽

Lucia Blasco ◽

Antón Ambroa ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Host Range ◽

Burst Size ◽

Three Dimensional ◽

Genomic Analysis ◽

Amino Acid Sequences ◽

Phylogenetic Study ◽

Tail Fiber ◽

Homing Endonucleases ◽

Query Cover

Klebsiella pneumoniae is a human pathogen that worsens the prognosis of many immunocompromised patients. Here, we annotated and compared the genomes of two lytic phages that infect clinical strains of K. pneumoniae (vB_KpnM-VAC13 and vB_KpnM-VAC66) and phenotypically characterized vB_KpnM-VAC66 (time of adsorption of 12 min, burst size of 31.49 ± 0.61 PFU/infected cell, and a host range of 20.8% of the tested strains). Transmission electronic microscopy showed that vB_KpnM-VAC66 belongs to the Myoviridae family. The genomic analysis of the phage vB_KpnM-VAC66 revealed that its genome encoded 289 proteins. When compared to the genome of vB_KpnM-VAC13, they showed a nucleotide similarity of 97.56%, with a 93% of query cover, and the phylogenetic study performed with other Tevenvirinae phages showed a close common ancestor. However, there were 21 coding sequences which differed. Interestingly, the main differences were that vB_KpnM-VAC66 encoded 10 more homing endonucleases than vB_KpnM-VAC13, and that the nucleotidic and amino-acid sequences of the L-shaped tail fiber protein were highly dissimilar, leading to different three-dimensional protein predictions. Both phages differed significantly in their host range. These viruses may be useful in the development of alternative therapies to antibiotics or as a co-therapy increasing its antimicrobial potential, especially when addressing multidrug resistant (MDR) pathogens.

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Cargo Transport Shapes the Spatial Organization of a Microbial Community

10.1101/318600 ◽

2018 ◽

Author(s):

Abhishek Shrivastava ◽

Visha K. Patel ◽

Yisha Tang ◽

Susan Connolly Yost ◽

Floyd E. Dewhirst ◽

...

Keyword(s):

Degrees Of Freedom ◽

Spatial Organization ◽

Single Cells ◽

Bacterial Species ◽

Three Dimensional ◽

Human Microbiome ◽

Genomic Analysis ◽

Oral Microbiome ◽

Gliding Bacteria ◽

Semi Solid

AbstractThe human microbiome is an assemblage of diverse bacteria that interact with one another to form communities. Bacteria in a given community are arranged in a three-dimensional matrix with many degrees of freedom. Snapshots of the community display well-defined structures, but the steps required for their assembly are not understood. Here, we show that this construction is carried out with the help of gliding bacteria. Gliding is defined as the motion of cells over a solid or semi-solid surface without the necessity of growth or the aid of pili or flagella. Genomic analysis suggests that gliding bacteria are present in human microbial communities. We focus on Capnocytophaga gingivalis which is present in abundance in the human oral microbiome. Tracking of fluorescently-labeled single cells and of gas bubbles carried by fluid flow shows that swarms of C. gingivalis are layered, with cells in the upper layers moving more rapidly than those in the lower layers. Thus, cells also glide on top of one another. Cells of non-motile bacterial species attach to the surface of C. gingivalis and are propelled as cargo. The cargo cell moves along the length of a C. gingivalis cell, looping from one pole to the other. Multi-color fluorescent spectral imaging of cells of different live but non-motile bacterial species reveals their long-range transport in a polymicrobial community. A swarm of C. gingivalis transports some non-motile bacterial species more efficiently than others and helps shape the spatial organization of a polymicrobial community.SignificanceWe describe a situation in which bacteria typical of the human oral microbiome are organized spatially by gliding cells, species of Capnocytophaga, that move backwards and forwards over the substratum. The mobile adhesins that pull the cells over the substratum also attach to cells of non-motile bacterial species, which are carried up and down the motile cells as cargo. The synchronized transport of non-motile cargo bacteria helps shape a polymicrobial community.

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