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Evaluation of a gene information summarization system by users during the analysis process of microarray datasets

Jianji Yang, Aaron Cohen, William Hersh
2009 BMC Bioinformatics  
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

Miguel Reboiro-Jato, Joel P Arrais, José Oliveira, Florentino Fdez-Riverola
2014 BMC Bioinformatics  
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

Yuerong Zhu, Yuelin Zhu, Wei Xu
2008 BMC Bioinformatics  
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

D.E. Maroulis, I.N. Flaounas, D.K. Iakovidis, S.A. Karkanis
2006 Computer Methods and Programs in Biomedicine  
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

Salvatore Alaimo, Antonio Di Maria, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti
2019 BMC Bioinformatics  
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:  ... 
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

Wei-Chung Cheng, Min-Lung Tsai, Cheng-Wei Chang, Ching-Lung Huang, Chaang-Ray Chen, Wun-Yi Shu, Yun-Shien Lee, Tzu-Hao Wang, Ji-Hong Hong, Chia-Yang Li, Ian C Hsu
2010 BMC Bioinformatics  
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

Alexander Statnikov, Ioannis Tsamardinos, Yerbolat Dosbayev, Constantin F. Aliferis
2005 International Journal of Medical Informatics  
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

A. Sallaberry, N. Pecheur, S. Bringay, M. Roche, M. Teisseire
2011 Journal of Biomedical Informatics  
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

Ming Yi, Jay D Horton, Jonathan C Cohen, Helen H Hobbs, Robert M Stephens
2006 BMC Bioinformatics  
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

Zhenguo Zhou
2012 Journal of Data Mining in Genomics & Proteomics  
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  
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

N. KannaiyaRaja, K. Arulandam, A. Senthamaraiselvan, K. Babu
2012 International Journal of Computer Applications  
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

Tomasz Waller, Tomasz Gubała, Krzysztof Sarapata, Monika Piwowar, Wiktor Jurkowski
2015 BioData Mining  
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

Todd Allen
2013 The Mathematica Journal  
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

Peijian Cao, Ki-Hong Jung, Daeseok Choi, Daehee Hwang, Jun Zhu, Pamela C Ronald
2012 Rice  
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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