An ensemble approach for gene regulatory network study in rice blast

Sarkar, Chiranjib; Parsad, Rajender; Mishra, Dwijesh Chandra; Rai, Anil

doi:10.22271/09746315.2020.v16.i3.1358

Cited by 2 publications

(3 citation statements)

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“…The mean and standard error (SE) are calculated as ( Sarkar et al, 2020 ):

where B is the number of Bootstrap samples.…”

Section: Program Description and Methodsmentioning

confidence: 99%

“…The p -values are combined using Fisher’s weighted method ( Hedges and Olkin, 2014 ) following the steps as given in Sarkar et al (2020) :

…”

Section: Program Description and Methodsmentioning

confidence: 99%

“…It allows users to provide their own gene expression data to get the significant edges and nodes of the GRN. In our web tool, we have used Fisher’s weighted method for combining the output of GRN obtained from correlation, principal component regression (PCR), partial least square (PLS), and ridge regression ( Sarkar et al, 2020 ). The data analysis part of computing the edge score from correlation, PCR, PLS, and ridge regression has been written in R programming language.…”

Section: Introductionmentioning

confidence: 99%

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A Web Tool for Consensus Gene Regulatory Network Construction

et al. 2021

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Gene regulatory network (GRN) construction involves various steps of complex computational steps. This step-by-step procedure requires prior knowledge of programming languages such as R. Development of a web tool may reduce this complexity in the analysis steps which can be easy accessible for the user. In this study, a web tool for constructing consensus GRN by combining the outcomes obtained from four methods, namely, correlation, principal component regression, partial least square, and ridge regression, has been developed. We have designed the web tool with an interactive and user-friendly web page using the php programming language. We have used R script for the analysis steps which run in the background of the user interface. Users can upload gene expression data for constructing consensus GRN. The output obtained from analysis will be available in downloadable form in the result window of the web tool.

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“…The mean and standard error (SE) are calculated as ( Sarkar et al, 2020 ):

where B is the number of Bootstrap samples.…”

Section: Program Description and Methodsmentioning

confidence: 99%

“…The p -values are combined using Fisher’s weighted method ( Hedges and Olkin, 2014 ) following the steps as given in Sarkar et al (2020) :

…”

Section: Program Description and Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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