scholarly journals Image Analysis Workflow for 2-D Electrophoresis Gels Based on ImageJ

2011 ◽  
Vol 4 ◽  
pp. PRI.S7971 ◽  
Author(s):  
Massimo Natale ◽  
Bernardetta Maresca ◽  
Paolo Abrescia ◽  
Enrico M. Bucci
Keyword(s):  
Life Sciences ◽  
National Institutes Of Health ◽  
Plasma Samples ◽  
Two Dimensional Electrophoresis ◽  
Standard Data ◽  
Software Packages ◽  
Commercial Package ◽  
Analysis Workflow ◽  
Analysis Application ◽  
Dimensional Electrophoresis

A number of commercial software packages are currently available to perform digital two-dimensional electrophoresis (2D-GE) gel analysis. However, both the high cost of the commercial packages and the unavailability of a standard data analysis workflow, have prompted several groups to develop freeware systems to perform certain steps of gel analysis. Unfortunately, to the best of our knowledge none of them offer a package that performs all the steps envisaged in a 2D-GE gel analysis. Here we describe an ImageJ-based procedure, able to manage all the steps of a 2D-GE gel analysis. ImageJ is a free available image processing and analysis application developed by National Institutes of Health (NIH) and widely used in different life sciences fields as medical imaging, microscopy, western blotting and PAGE. Nevertheless no one has yet developed a procedure enabled to compare spots on 2D-GE gels. We collected all used ImageJ tools in a plug-in that allows us to perform the whole 2D-GE analysis. To test it, we performed a set of 2D-GE experiments on plasma samples from 9 patients victims of acute myocardial infarction and 8 controls, and we compared the results obtained by our procedure to those obtained using a widely diffuse commercial package, finding similar performances.

scholarly journals A Robust Identification of the Protein Standard Bands in Two-Dimensional Electrophoresis Gel Images

2017 ◽  
Vol 13 (1) ◽  
pp. 63-68
Author(s):  
Artūras Serackis ◽  
Dalius Matuzevičius ◽  
Dalius Navakauskas ◽  
Eldar Šabanovič ◽  
Andrius Katkevičius ◽  
...  
Keyword(s):  
Image Features ◽  
Self Organizing Map ◽  
Two Dimensional ◽  
Robust Identification ◽  
Two Dimensional Electrophoresis ◽  
Unknown Protein ◽  
Analysis Workflow ◽  
Dimensional Electrophoresis ◽  
New Algorithms

Abstract The aim of the investigation presented in this paper was to develop a software-based assistant for the protein analysis workflow. The prior characterization of the unknown protein in two-dimensional electrophoresis gel images is performed according to the molecular weight and isoelectric point of each protein spot estimated from the gel image before further sequence analysis by mass spectrometry. The paper presents a method for automatic and robust identification of the protein standard band in a two-dimensional gel image. In addition, the method introduces the identification of the positions of the markers, prepared by using pre-selected proteins with known molecular mass. The robustness of the method was achieved by using special validation rules in the proposed original algorithms. In addition, a self-organizing map-based decision support algorithm is proposed, which takes Gabor coefficients as image features and searches for the differences in preselected vertical image bars. The experimental investigation proved the good performance of the new algorithms included into the proposed method. The detection of the protein standard markers works without modification of algorithm parameters on two-dimensional gel images obtained by using different staining and destaining procedures, which results in different average levels of intensity in the images.

scholarly journals Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists

2015 ◽  
Vol 9 ◽  
pp. BBI.S12467 ◽  
Author(s):  
Xiaoxi Dong ◽  
Anatoly Yambartsev ◽  
Stephen A. Ramsey ◽  
Lina D Thomas ◽  
Natalia Shulzhenko ◽  
...  
Keyword(s):  
Big Data ◽  
Network Analysis ◽  
Regulatory Networks ◽  
Life Sciences ◽  
Massively Parallel ◽  
Biological Knowledge ◽  
Software Packages ◽  
Analysis Workflow ◽  
Functional Pathways ◽  
Cancer Network

Omics technologies enable unbiased investigation of biological systems through massively parallel sequence acquisition or molecular measurements, bringing the life sciences into the era of Big Data. A central challenge posed by such omics datasets is how to transform these data into biological knowledge, for example, how to use these data to answer questions such as: Which functional pathways are involved in cell differentiation? Which genes should we target to stop cancer? Network analysis is a powerful and general approach to solve this problem consisting of two fundamental stages, network reconstruction, and network interrogation. Here we provide an overview of network analysis including a step-by-step guide on how to perform and use this approach to investigate a biological question. In this guide, we also include the software packages that we and others employ for each of the steps of a network analysis workflow.

scholarly journals Reverse enGENEering of regulatory networks from Big Data: a guide for a biologist

2014 ◽  
Author(s):  
Andrey Morgun ◽  
Xiaoxi Dong ◽  
Anatoly Yambartsev ◽  
Stephen Ramsey ◽  
lina Thomas ◽  
...  
Keyword(s):  
Big Data ◽  
Network Analysis ◽  
Regulatory Networks ◽  
Life Sciences ◽  
Massively Parallel ◽  
Biological Knowledge ◽  
Software Packages ◽  
Analysis Workflow ◽  
Functional Pathways ◽  
Cancer Network

Omics technologies enable unbiased investigation of biological systems through massively parallel sequence acquisition or molecular measurements, bringing the life sciences into the era of Big Data. A central challenge posed by such omics datasets is how to transform this data into biological knowledge. For example, how to use this data to answer questions such as: which functional pathways are involved in cell differentiation? Which genes should we target to stop cancer? Network analysis is a powerful and general approach to solve this problem consisting of two fundamental stages, network reconstruction and network interrogation. Herein, we provide an overview of network analysis including a step by step guide on how to perform and use this approach to investigate a biological question. In this guide, we also include the software packages that we and others employ for each of the steps of a network analysis workflow.

Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels

PROTEOMICS ◽  
2003 ◽  
Vol 3 (10) ◽  
pp. 1936-1946 ◽  
Author(s):  
Arsi T. Rosengren ◽  
Jussi M. Salmi ◽  
Tero Aittokallio ◽  
Jan Westerholm ◽  
Riitta Lahesmaa ◽  
...  
Keyword(s):  
Two Dimensional ◽  
Two Dimensional Electrophoresis ◽  
Software Packages ◽  
Dimensional Electrophoresis

Sialic Acid Dependent Polypeptide Chain Heterogeneity of Human Fibrinogen Demonstrated by Two-Dimensional Electrophoresis

1982 ◽  
Vol 47 (01) ◽  
pp. 019-021 ◽  
Author(s):  
Cemal Kuyas ◽  
André Haeberli ◽  
P Werner Straub
Keyword(s):  
Sialic Acid ◽  
Polypeptide Chain ◽  
Two Dimensional ◽  
Charge Heterogeneity ◽  
Human Fibrinogen ◽  
Two Dimensional Electrophoresis ◽  
Isoelectric Points ◽  
Polypeptide Chains ◽  
Dimensional Electrophoresis ◽  
Chain Type

SummaryHuman fibrinogen was compared with asialofibrinogen by two-dimensional electrophoresis to evaluate the contribution of sialic acid to the heterogeneity of the γ- and Bβ-polypeptide chains.Reduced fibrinogen showed three major variants for both the γ- and Bβ-chains. In addition two minor γ-bands with a more acidic isoelectric point than the normal γ-chains were observed. Electrophoresis in the second dimension (SDS) suggests that these most acidic bands are γ-chain-variants with a higher molecular weight. In asialofibrinogen only two predominant variants with more alkaline isoelectric points were present in each chain type.It is concluded that enzymatic removal of sialic acid partially reduces the heterogeneity of the γ- and Bβ-polypeptide chains of human fibrinogen, but additional sources producing charge heterogeneity must be sought.

Improvement of Two-dimensional Electrophoresis of Rice (Oryza sativaL.) Proteomics

2012 ◽  
Vol 18 (5) ◽  
pp. 819 ◽  
Author(s):  
Yanhua YANG ◽  
Weitong CUI ◽  
Xiaoyong LIU ◽  
Keming ZHU ◽  
Keping CHEN
Keyword(s):  
Two Dimensional ◽  
Two Dimensional Electrophoresis ◽  
Dimensional Electrophoresis
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