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Evaluation of a gene information summarization system by users during the analysis process of microarray datasets
2009
BMC Bioinformatics
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The Gene Information Clustering and Summarization System (GICSS) is a system that integrates two related steps of the microarray data analysis process: functional gene clustering and gene information gathering ...
The system evaluation was conducted during the process of genomic researchers analyzing their own experimental microarray datasets. ...
Focusing on the analysis of differentially expressed gene sets from microarray data, the Gene Information Clustering and Summarization System (GICSS) consists of a two-step process. ...
doi:10.1186/1471-2105-10-s2-s5
pmid:19208193
pmcid:PMC2646238
fatcat:z5mt6cea7vbhfapef6b7is2aj4
geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification
2014
BMC Bioinformatics
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In this context, microarrays can generate expression data for a huge set of genes. ...
Conclusions: geneCommittee allows the enrichment of microarrays raw data with gene functional annotations, producing integrated datasets that simplify the construction of better discriminative hypothesis ...
The evaluation result can be easily inspected by the user with the goal of selecting those classifiers that best discriminate the train dataset. ...
doi:10.1186/1471-2105-15-31
pmid:24475928
pmcid:PMC3909759
fatcat:5avybdr4ozblnnhjvy7ssicwga
EzArray: A web-based highly automated Affymetrix expression array data management and analysis system
2008
BMC Bioinformatics
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Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. ...
Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. ...
Acknowledgements Wei Xu was supported in part by Susan Komen Breast Cancer Foundation grant number BCTR95306. We would like to thank Emily Powell for the critical review the manuscript. ...
doi:10.1186/1471-2105-9-46
pmid:18218103
pmcid:PMC2265266
fatcat:qalzwdqtsbgahhxt4jhborcqse
Microarray-MD: A system for exploratory analysis of microarray gene expression data
2006
Computer Methods and Programs in Biomedicine
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software system that is able to assist in the exploratory analysis of gene expression microarray data. ...
A graphical user interface provides easy access to the system operations and direct adjustment of its parameters. It has been tested on various publicly available datasets. ...
., University of Athens, Medical School and his research group for their effort on the evaluation of the Microarray-MD system and their substantial suggestions. ...
doi:10.1016/j.cmpb.2006.06.008
pmid:16893587
fatcat:orbeie7cdjg4xjgfb26n4fenem
TACITuS: transcriptomic data collector, integrator, and selector on big data platform
2019
BMC Bioinformatics
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TACITuS automates most of the pre-processing needed to analyze high-throughput microarray and NGS data from large publicly-available repositories. ...
The system also supports the ability to import data into Galaxy for further analysis. ...
Acknowledgements The results presented in this manuscript are in part based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/. ...
doi:10.1186/s12859-019-2912-4
pmid:31757212
pmcid:PMC6873396
fatcat:exzinawmqzds3ismxor7nigl2y
Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
2010
BMC Bioinformatics
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Meta-analysis of substantial amounts of accumulated data, by integrating valuable information from multiple studies, is becoming more important in microarray research. ...
This database provides a lower entry threshold and an integrated process of meta-analysis. We hope that this research will promote further evolution of microarray meta-analysis. ...
Acknowledgements We are grateful to the National Center for High-performance Computing for computer time and facilities. ...
doi:10.1186/1471-2105-11-421
pmid:20698961
pmcid:PMC2928207
fatcat:b73by765s5f2nldjn3mzraoi4y
GEMS: A system for automated cancer diagnosis and biomarker discovery from microarray gene expression data
2005
International Journal of Medical Informatics
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In this paper we present a preliminary evaluation of the system with five new datasets. ...
The performance of the models produced automatically by GEMS is comparable or better than the results obtained by human analysts. Additionally, we performed a cross-dataset evaluation of the system. ...
Acknowledgements This research was supported by NIH grants RO1 LM007948-01 and P20 LM 007613-01. We also acknowledge all developers of the systems listed in Table 1 for access to their software. ...
doi:10.1016/j.ijmedinf.2005.05.002
pmid:15967710
fatcat:7hcpdietubd4xdim2v37qja4km
Sequential patterns mining and gene sequence visualization to discover novelty from microarray data
2011
Journal of Biomedical Informatics
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In this paper, we focus on sequential pattern mining and propose a new visualization system to help end users analyze the extracted knowledge and to highlight novelty according to databases of referenced ...
Sequential patterns extracted from gene data using our system were successfully evaluated by two biology laboratories working on Alzheimer's disease and cancer. ...
We would also like to thank the members of the Pikko company who provided our material resources. ...
doi:10.1016/j.jbi.2011.04.002
pmid:21527357
fatcat:ln5lronsxbbdhbai5wapcqtsum
WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data
2006
BMC Bioinformatics
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We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. ...
Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. ...
Initial funding came from The Howard Hughes Medical Institute and the National Institute of Health (ROI HL72304 and NHLBI Program for Genomic Applications UOI HL66880). ...
doi:10.1186/1471-2105-7-30
pmid:16423281
pmcid:PMC1388242
fatcat:kicl3pjrlzbztf6seuxws32izy
OmicsMiner: A Biological Data Mining Framework
2012
Journal of Data Mining in Genomics & Proteomics
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Abstract OmicsMiner is a computational platform providing systematic access to state-of-the-art data processing and mining methods with the goal of facilitating the design of customized pipelines for processing ...
OmicsMiner also provides convenient and concise interactive graphical user interfaces for data processing. OmicsMiner is a Java program that is platform-independent and does not require installation. ...
Acknowledgements This work was supported by award number P20 RR016475 from the National Center for Research Resources, by award number R01 HD061580 from the National Institute of Child Health & Human Development ...
doi:10.4172/2153-0602.1000115
fatcat:g76hialukbaenlrj7vjtf3qgyq
Interpreting the gene expression microarray results: a user-based evaluation of 10 bioinformatics tools
2013
Archives Italiennes de Biologie
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In this paper, ten tools for the interpretation of gene expression microarray results have been tested on eleven microarray datasets and evaluated according to eight assessment criteria: 1. interface design ...
Strengths and weaknesses of each tool are highlighted: a. to provide useful tips to users dealing with the biological interpretation of microarray results; b. to draw the attention of software developers ...
Acknowledgements EM was supported by a grant from the Italian Research Ministry (PRIN 2008). VM was supported by the Interdepartmental Research Center "E. Piaggio", University of Pisa. ...
doi:10.12871/00039829201324
fatcat:f5leigbfrfgppbezxnzbiw6pwa
LONETSSOM Platform: Enabling Distributed Processing, Managing and Mining of Biological Data through Fusion of Logical Network and Web Technologies in NETWORK Infrastructure
2012
International Journal of Computer Applications
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LONETSSOM), and a web based application that exploits logical management systems and distributed data processing system are highly used for DNA microarray through a genetic consistent, computational analysis ...
The advanced framework of logical network system is LONETSSOM which perform efficient versatile annotation system and integrative analysis through multi-application programming interface delivered in the ...
We wish to thank the ICJA Publisher and the entire team of ICJA Publication for their suggestion and support. ...
doi:10.5120/4793-7042
fatcat:rtablnccp5fq7o2hxzkebf3vsi
DNA microarray integromics analysis platform
2015
BioData Mining
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The first test case involves the analysis of the nutrimouse dataset, which contains measurements of the expression of genes involved in nutritional problems and the concentrations of hepatic fatty acids ...
Conclusions: The DNA Microarray Integromics Analysis Platform is a web-based graphical user interface for "multi-omics" data management and analysis. ...
Acknowledgements The DNA Microarray Integromics Analysis Platform was developed in the scope of the PLGrid Plus project, which was co-financed by the European Union (under the Innovative Economy Fund). ...
doi:10.1186/s13040-015-0052-6
pmid:26110022
pmcid:PMC4479227
fatcat:gzttuy2yl5fjnpdnt3ohcfykvm
Detecting Differential Gene Expression Using Affymetrix Microarrays
2013
The Mathematica Journal
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between the probes 4. summarization: performed to obtain a single measure of gene expression from the multiple measurements obtained by each probeset; this process often attempts to correct "probe" and ...
After the probesets are summarized, the differential expression of each gene is obtained by subtracting the expression of a gene in the control condition from the expression of the gene in the experimental ...
His interest in computational biology using Mathematica took shape during his postdoctoral research years at the University of Maryland, where he developed a custom cDNA microarray chip to study gene expression ...
doi:10.3888/tmj.15-11
fatcat:z7f2mmp6uncbleikhq3u6mqrxe
The Rice Oligonucleotide Array Database: an atlas of rice gene expression
2012
Rice
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The ROAD's user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. ...
Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. ...
As a result, an increasing number of rice microarray datasets are being deposited in public repositories such as the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information ( ...
doi:10.1186/1939-8433-5-17
pmid:24279809
pmcid:PMC4883718
fatcat:vkuck46sqjaw3abye4ujhuqmc4
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