scholarly journals TbasCO: Trait-based Comparative ’Omics Identifies Ecosystem-Level and Niche- Differentiating Adaptations of an Engineered Microbiome

2021 ◽  
Author(s):  
E.A. McDaniel ◽  
J.J.M van Steenbrugge ◽  
D.R. Noguera ◽  
K.D. McMahon ◽  
J.M. Raaijmakers ◽  
...  
Keyword(s):  
Kegg Pathway ◽  
Marker Genes ◽  
Grand Challenge ◽  
Biological Phosphorus Removal ◽  
Pathway Database ◽  
Kegg Pathway Database ◽  
Metabolic Versatility ◽  
Transcriptional Pattern ◽  
Ecosystem Level ◽  
Biological Phosphorus

ABSTRACTA grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while 14 genomes containing the high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by 11 genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for revealing hidden metabolic versatility when investigating genomic data alone by assigning trait-attributes through genome-resolved time-series metatranscriptomics.

scholarly journals Meta-Analysis of Differential miRNA Expression after Bariatric Surgery

2019 ◽  
Vol 8 (8) ◽  
pp. 1220 ◽  
Author(s):  
Gladys Langi ◽  
Lukasz Szczerbinski ◽  
Adam Kretowski
Keyword(s):  
Bariatric Surgery ◽  
Target Genes ◽  
Web Of Science ◽  
Kegg Pathway ◽  
Meta Analysis ◽  
Obese Patients ◽  
Pathway Database ◽  
Efficient Treatment ◽  
Kegg Pathway Database ◽  
Before And After

Bariatric surgery is an efficient treatment for weight loss in obese patients and for resolving obesity comorbidities. However, the mechanisms behind these outcomes are unclear. Recent studies have indicated significant alterations in the transcriptome after surgery, specifically in the differential expression of microRNAs. In order to summarize the recent findings, we conducted a systematic summary of studies comparing microRNA expression levels before and after surgery. We identified 17 animal model and human studies from four databases (Ovid, Scopus, Web of Science, and PubMed) to be enrolled in this meta-analysis. From these studies, we identified 14 miRNAs which had the same direction of modulation of their expression after surgery in at least two studies (downregulated: hsa-miR-93-5p, hsa-miR-106b-5p, hsa-let-7b-5p, hsa-let-7i-5p, hsa-miR-16-5p, hsa-miR-19b-3p, hsa-miR-92a-3p, hsa-miR-222-3p, hsa-miR-142-3p, hsa-miR-140-5p, hsa-miR-155-5p, rno-miR-320-3p; upregulated: hsa-miR-7-5p, hsa-miR-320c). Pathway analysis for these miRNAs was done using database resources (DIANA-TarBase and KEGG pathway database) and their predicted target genes were discussed in relation with obesity and its comorbidities. Discrepancies in study design, such as miRNA source, bariatric surgery type, time of observation after surgery, and miRNA profiling methods, were also discussed.

Chemogenomic analysis of neuronal differentiation with pathway changes in PC12 cells

2016 ◽  
Vol 12 (1) ◽  
pp. 283-294 ◽  
Author(s):  
Jack Yu-Shih Lin ◽  
Chien Liang Wu ◽  
Chia Nan Liao ◽  
Akon Higuchi ◽  
Qing-Dong Ling
Keyword(s):  
Molecular Biology ◽  
Neuronal Differentiation ◽  
Pc12 Cells ◽  
Kegg Pathway ◽  
Chemical Elements ◽  
Pathway Database ◽  
Kegg Pathway Database

The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database creates networks from interrelations between molecular biology and underlying chemical elements.

scholarly journals KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

2011 ◽  
Vol 27 (16) ◽  
pp. 2314-2315 ◽  
Author(s):  
Clemens Wrzodek ◽  
Andreas Dräger ◽  
Andreas Zell
Keyword(s):  
Kegg Pathway ◽  
Pathway Database ◽  
Kegg Pathway Database

scholarly journals CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 145 ◽  
Author(s):  
Lilit Nersisyan ◽  
Ruben Samsonyan ◽  
Arsen Arakelyan
Keyword(s):  
Systems Biology ◽  
Protein Interaction ◽  
Kegg Pathway ◽  
Computer Assisted ◽  
Pathway Database ◽  
Protein Protein Interaction ◽  
Kegg Pathways ◽  
Kegg Pathway Database ◽  
Context Specific ◽  
Biological Context

The KEGG pathway database is a widely accepted source for biomolecular pathway maps. In this paper we present the CyKEGGParser app (http://apps.cytoscape.org/apps/cykeggparser) for Cytoscape 3 that allows manipulation with KEGG pathway maps. Along with basic functionalities for pathway retrieval, visualization and export in KGML and BioPAX formats, the app provides unique features for computer-assisted adjustment of inconsistencies in KEGG pathway KGML files and generation of tissue- and protein-protein interaction specific pathways. We demonstrate that using biological context-specific KEGG pathways created with CyKEGGParser makes systems biology analysis more sensitive and appropriate compared to original pathways.

Computation with the KEGG pathway database

Biosystems ◽  
1998 ◽  
Vol 47 (1-2) ◽  
pp. 119-128 ◽  
Author(s):  
Hiroyuki Ogata ◽  
Susumu Goto ◽  
Wataru Fujibuchi ◽  
Minoru Kanehisa
Keyword(s):  
Kegg Pathway ◽  
Pathway Database ◽  
Kegg Pathway Database

scholarly journals Local delivery of FTY720 induces neutrophil activation through chemokine signaling in an oronasal fistula model

2021 ◽  
Author(s):  
AM Amanso ◽  
TC Turner ◽  
A Kamalakar ◽  
SA Ballestas ◽  
LA Hymel ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Kegg Pathway ◽  
Vehicle Control ◽  
Local Delivery ◽  
Sequencing Analysis ◽  
Pathway Database ◽  
Kegg Pathway Database ◽  
Oronasal Fistula ◽  
Mucosal Defect ◽  
Chemokine Signaling

Abstract Purpose Cleft palate repair surgeries lack a regenerative reconstructive option and, in many cases, develop complications including oronasal fistula (ONF). Our group has developed a novel murine phenocopy of ONF to study the oral cavity wound healing program. Using this model, our team previously identified that delivery of FTY720 on a nanofiber scaffold had a unique immunomodulatory effect directing macrophages and monocytes into a pro-regenerative state during ONF healing. Here, the objective of this study was to determine the effects of local biomaterial-based FTY720 delivery in the ONF model on the early bulk gene expression and neutrophil phenotypic response within the regenerating tissue. Methods Using a mouse model of ONF formation, a palate defect was created and was treated with FTY720 nanofiber scaffolds or (blank) vehicle control nanofibers. At 1 and 3 days post-implantation, ONF oral mucosal tissue from the defect region was collected for RNA sequencing analysis or flow cytometry. For the RNA-seq expression profiling, intracellular pathways were assessed using the KEGG Pathway database and Gene Ontology (GO) Terms enrichment interactive graph. To assess the effects of FTY720 on different neutrophil subpopulations, flow cytometry data was analyzed using pseudotime analysis based on Spanning-tree Progression Analysis of Density-normalized Events (SPADE). Results RNA sequencing analysis of palate mucosa injured tissue identified 669 genes that were differentially expressed (DE) during the first 3 days of ONF wound healing after local delivery of FTY720, including multiple genes in the sphingolipid signaling pathway. Evaluation of the DE genes at the KEGG Pathway database also identified the inflammatory immune response pathways (chemokine signaling, cytokine-cytokine receptor interaction, and leukocyte transendothelial migration), and the Gene Ontology enrichment analysis identified neutrophil chemotaxis and migration terms. SPADE dendrograms of CD11b+Ly6G+ neutrophils at both day 1 and day 3 post-injury showed significantly distinct subpopulations of neutrophils in oral mucosal defect tissue from the FTY720 scaffold treatment group compared to the vehicle control group (blank). Increased expression of CD88 and Vav1, among other genes, were found and staining of the ONF area demonstrated increased VAV1 staining in FTY720‐treated healing oral mucosa. Conclusion Treatment of oral mucosal defects using FTY720 scaffolds is a promising new immunotherapy to improve healing outcomes and reducing ONF formation during cleft palate surgical repair. Local delivery of FTY720 nanofiber scaffolds during ONF healing significantly shifted early gene transcription associated with immune cell recruitment and modulation of the immune microenvironment results in distinct neutrophil subpopulations in the oral mucosal defect tissue that provides a critical shift toward pro-regenerative immune signaling.

scholarly journals Anthraquinone derivatives as an immune booster and their therapeutic option against COVID-19

2020 ◽  
Author(s):  
Pukar Khanal ◽  
BM Patil ◽  
Jagdish chand ◽  
Yasmin Naaz
Keyword(s):  
Binding Affinity ◽  
Kegg Pathway ◽  
Therapeutic Option ◽  
Docking Study ◽  
Spike Protein ◽  
Pathway Database ◽  
Kegg Pathway Database ◽  
Anthraquinone Derivatives ◽  
Novel Coronavirus ◽  
Immune Booster

Abstract Multiple Anthraquinolines derivatives are reported for their immune-boosting, anti-inflammatory and anti-viral efficacy. Hence, the present study dealt to investigate the reported anthraquinone derivatives as an immune booster molecule in COVID-19 infection and evaluate their binding affinity with three reported targets of novel coronavirus i.e. 3CLpro, PLpro and spike proteins. The reported anthraquinone derivatives were retrieved from an open-source database and filtered based on a positive druglikeness score. Further, the probably modulated gene by compounds with positive druglikeness score was evaluated for the modulation of proteins using DIGEP-Pred and the interaction of proteins was evaluated using STRING; associated pathways were recorded concerning the KEGG pathway database. Finally, docking was carried using autodock4; pose scoring minimum binding energy was chosen to visualize the ligand-protein interaction. Among 101 compounds, 36 scored positive druglikeness scores; modulating multiple pathways for immune-boosting as well as pathways involved in infectious and non-infectious diseases. Similarly, docking study revealed torososide B to have the highest binding affinity with PLpro and 3clpro and 1,3,6-trihydroxy-2-methyl-9,10-anthraquinone-3-O-(6'-O-acetyl)-β-D-xylopyranosyl-(1->2)-β-D-glucopyranoside with spike protein

scholarly journals KPGminer: A tool for retrieving pathway genes from KEGG pathway database

2018 ◽  
Author(s):  
A. K. M. Azad
Keyword(s):  
Pathway Analysis ◽  
Kegg Pathway ◽  
Single Mode ◽  
Computational Systems Biology ◽  
Pathway Database ◽  
Batch Mode ◽  
Kegg Pathways ◽  
Kegg Pathway Database ◽  
Crucial Component ◽  
Computational Systems

AbstractPathway analysis is a very important aspect in computational systems biology as it serves as a crucial component in many computational pipelines. KEGG is one of the prominent databases that host pathway information associated with various organisms. In any pathway analysis pipelines, it is also important to collect and organize the pathway constituent genes for which a tool to automatically retrieve that would be a useful one to the practitioners. In this article, I present KPGminer, a tool that retrieves the constituent genes in KEGG pathways for various organisms and organizes that information suitable for many downstream pathway analysis pipelines. We exploited several KEGG web services using REST APIs, particularly GET and LIST methods to request for the information retrieval which is available for developers. Moreover, KPGminer can operate both for a particular pathway (single mode) or multiple pathways (batch mode). Next, we designed a crawler to extract necessary information from the response and generated outputs accordingly. KPGminer brings several key features including organism-specific and pathway-specific extraction of pathway genes from KEGG and always up-to-date information. Thus, we hope KPGminer can be a useful and effective tool to make downstream pathway analysis easier and faster. KPGminer is freely available for download from https://sourceforge.net/projects/kpgminer/.

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