ArticleFrontiers in genetics2019
Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis.
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis that pooled it.
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Who cites it
54 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
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- Exploring effector candidates in Rhynchosporium commune: insights into their expression dynamics during barley infection.Scientific reports · 2025Article
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- Transcriptomic Analysis During the Induction of Somatic Embryogenesis in Coffea canephora.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Alternative splicing events as peripheral biomarkers for motor learning deficit caused by adverse prenatal environments.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Asterics: a simple tool for the ExploRation and Integration of omiCS data.BMC bioinformatics · 2023Article
- Data Mining of Microarray Datasets in Translational Neuroscience.Brain sciences · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The current DNA sequencing technologies and their high-throughput yield, allowed the thrive of genomic and transcriptomic experiments but it also have generated big data problem. Due to this exponential growth of sequencing data, also the complexity of managing, processing and interpreting it in order to generate results, has raised. Therefore, the demand of easy-to-use friendly software and websites to run bioinformatic tools is imminent. In particular, RNA-Seq and differential expression analysis have become a popular and useful method to evaluate the genetic expression change in any organism. However, many scientists struggle with the data analysis since most of the available tools are implemented in a UNIX-based environment. Therefore, we have developed the web server IDEAMEX (Integrative Differential Expression Analysis for Multiple EXperiments). The IDEAMEX pipeline needs a raw count table for as many desired replicates and conditions, allowing the user to select which conditions will be compared, instead of doing all-vs.-all comparisons. The whole process consists of three main steps (1) Data Analysis: that allows a preliminary analysis for quality control based on the data distribution per sample, using different types of graphs; (2) Differential expression: performs the differential expression analysis with or without batch effect error awareness, using the bioconductor packages, NOISeq, limma-Voom, DESeq2 and edgeR, and generate reports for each method; (3) Result integration: the obtained results the integrated results are reported using different graphical outputs such as correlograms, heatmaps, Venn diagrams and text lists. Our server allows an easy and friendly visualization for results, providing an easy interaction during the analysis process, as well as error tracking and debugging by providing output log files. The server is currently available and can be accessed at http://www.uusmb.unam.mx/ideamex/ where the documentation and example input files are provided. We consider that this web server can help other researchers with no previous bioinformatic knowledge, to perform their analyses in a simple manner.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.