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.

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/.

scholarly journals Simulation and visualization of multiple KEGG pathways using BioNSi

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 2120
Author(s):  
Adva Yeheskel ◽  
Adam Reiter ◽  
Metsada Pasmanik-Chor ◽  
Amir Rubinstein
Keyword(s):  
Network Simulation ◽  
Expression Data ◽  
Proof Of Concept ◽  
Pathway Database ◽  
Simulation Tools ◽  
Kegg Pathways ◽  
Kegg Pathway Database ◽  
Disease Condition ◽  
Inflammatory Bowel ◽  
Experimental Expression

Motivation: Many biologists are discouraged from using network simulation tools because these require manual, often tedious network construction. This situation calls for building new tools or extending existing ones with the ability to import biological pathways previously deposited in databases and analyze them, in order to produce novel biological insights at the pathway level. Results: We have extended a network simulation tool (BioNSi), which now allows merging of multiple pathways from the KEGG pathway database into a single, coherent network, and visualizing its properties. Furthermore, the enhanced tool enables loading experimental expression data into the network and simulating its dynamics under various biological conditions or perturbations. As a proof of concept, we tested two sets of published experimental data, one related to inflammatory bowel disease condition and the other to breast cancer treatment. We predict some of the major observations obtained following these laboratory experiments, and provide new insights that may shed additional light on these results. Tool requirements: Cytoscape 3.x, JAVA 8 Availability: The tool is freely available at http://bionsi.wix.com/bionsi, where a complete user guide and a step-by-step manual can also be found.

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.

scholarly journals Analysing Complex Oral Protein Samples: Complete Workflow and Case Analysis of Salivary Pellicles

2021 ◽  
Vol 10 (13) ◽  
pp. 2801
Author(s):  
Chen-Xuan Wei ◽  
Michael Francis Burrow ◽  
Michael George Botelho ◽  
W. Keung Leung
Keyword(s):  
Gene Ontology ◽  
Protein Interaction ◽  
Protein Identification ◽  
Protein Quantification ◽  
Structural Genomic ◽  
Protein Protein Interaction ◽  
Functional Connections ◽  
Salivary Pellicle ◽  
Complex Protein ◽  
Biological Context

Studies on small quantity, highly complex protein samples, such as salivary pellicle, have been enabled by recent major technological and analytical breakthroughs. Advances in mass spectrometry-based computational proteomics such as Multidimensional Protein Identification Technology have allowed precise identification and quantification of complex protein samples on a proteome-wide scale, which has enabled the determination of corresponding genes and cellular functions at the protein level. The latter was achieved via protein-protein interaction mapping with Gene Ontology annotation. In recent years, the application of these technologies has broken various barriers in small-quantity-complex-protein research such as salivary pellicle. This review provides a concise summary of contemporary proteomic techniques contributing to (1) increased complex protein (up to hundreds) identification using minute sample sizes (µg level), (2) precise protein quantification by advanced stable isotope labelling or label-free approaches and (3) the emerging concepts and techniques regarding computational integration, such as the Gene Ontology Consortium and protein-protein interaction mapping. The latter integrates the structural, genomic, and biological context of proteins and genes to predict protein interactions and functional connections in a given biological context. The same technological breakthroughs and computational integration concepts can also be applied to other low-volume oral protein complexes such as gingival crevicular or peri-implant sulcular fluids.

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.

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