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Probabilistic retrieval and visualization of biologically relevant microarray experiments

José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski
2009 BMC Bioinformatics  
Several case studies performed on a subset of ArrayExpress show that our method can retrieve experiments relevant to a biological question, as long as sufficient amounts of data are available, and highlight  ...  The visualization methods allow us to both efficiently interpret the model and put retrieval results in the context of the whole set of experiments (see Figure 1 for an example).  ...  JC, AF and SK are additionally partially supported by PASCAL 2 Network of Excellence, ICT 216886.  ... 
doi:10.1186/1471-2105-10-s13-p1 fatcat:u4o2wgmarjb5flo7at4kmi3fp4

Probabilistic retrieval and visualization of biologically relevant microarray experiments

J. Caldas, N. Gehlenborg, A. Faisal, A. Brazma, S. Kaski
2009 Bioinformatics  
Several case studies performed on a subset of ArrayExpress show that our method can retrieve experiments relevant to a biological question, as long as sufficient amounts of data are available, and highlight  ...  The visualization methods allow us to both efficiently interpret the model and put retrieval results in the context of the whole set of experiments (see Figure 1 for an example).  ...  JC, AF and SK are additionally partially supported by PASCAL 2 Network of Excellence, ICT 216886.  ... 
doi:10.1093/bioinformatics/btp215 pmid:19477980 pmcid:PMC2687969 fatcat:w4m3su325nh3nhqikouuohjthu

Dimensionality Reduction for Data Visualization [Applications Corner]

Samuel Kaski, Jaakko Peltonen
2011 IEEE Signal Processing Magazine  
[ FIG3] A visual information retrieval interface to a collection of microarray experiments visualized as glyphs on a plane (from [14]).  ...  APPLICATION 1: VISUALIZATION OF GENE EXPRESSION COMPENDIA FOR RETRIEVING RELEVANT EXPERIMENTS In the study of molecular biological systems, behavior of the system can seldom be inferred from first principles  ... 
doi:10.1109/msp.2010.940003 fatcat:2rufhzzxpjevbc6zf3pbuykize

SpaCEM3: a software for biological module detection when data is incomplete, high dimensional and dependent

M. Vignes, J. Blanchet, D. Leroux, F. Forbes
2011 Bioinformatics  
Conflict of Interest: none declared.  ...  This tackles the missing value issue in microarrays in a probabilistic framework and still enables a posteriori inference of incomplete observations without imposing any pre-processing of the data.  ...  First, data are retrieved from relevant databases to set a network topology or neighbourhood between biological components M.Vignes et al.  ... 
doi:10.1093/bioinformatics/btr034 pmid:21296754 pmcid:PMC3051335 fatcat:j7mukelnabge7ee6kbdbzctxyu

Semantic Subgroup Discovery and Cross-Context Linking for Microarray Data Analysis [chapter]

Igor Mozetič, Nada Lavrač, Vid Podpečan, Petra Kralj Novak, Helena Motaln, Marko Petek, Kristina Gruden, Hannu Toivonen, Kimmo Kulovesi
2012 Lecture Notes in Computer Science  
These genes are then contextualized by the computation of probabilistic links to diverse bioinformatics resources. Preliminary experiments with microarray data illustrate the approach.  ...  In the article we explore these ideas on the problem of analysis of microarray data.  ...  Finally, it estimates the relevance (or significance) of the automatically formulated hypotheses on experimental microarray data.  ... 
doi:10.1007/978-3-642-31830-6_27 fatcat:ros55glzj5aktly7fzyycdnf7u

Getting Started in Biological Pathway Construction and Analysis

Ganesh A Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman, Stuart C Sealfon, Olga Troyanskaya
2008 PLoS Computational Biology  
GAV, JS, SP, GN, and SCS wrote the paper. Funding. Our pathway research is supported by US National Institutes of Health NIAID contract HHSN2662000500021C.  ...  data, (e.g., MIAME, Minimal Information Associated with Microarray Experiments).  ...  Data-driven pathway construction is used to generate relationship information of genes or proteins identified in a specific experiment such as a microarray study.  ... 
doi:10.1371/journal.pcbi.0040016 pmid:18463709 pmcid:PMC2323403 fatcat:dldyxs5cdbabpbf23srfddtbye

Classification of information fusion methods in systems biology

Jane Synnergren, Björn Olsson, Jonas Gamalielsson
2009 In Silico Biology  
Biological systems are extremely complex and often involve thousands of interacting components. Despite all efforts, many complex biological systems are still poorly understood.  ...  We here review representative examples of bioinformatic methods for fusion-oriented interpretation of multiple heterogeneous biological data, and propose a classification into three categories of tasks  ...  retrieval, organization, visualization and statistical analysis of large sets of genes.  ... 
pmid:19795566 fatcat:fnri743i7nfwhg6ch327ewevmq

INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis

B. Coessens
2003 Nucleic Acids Research  
The tools allow normalization, filtering and clustering of microarray data, functional scoring of gene clusters, sequence retrieval, and detection of known and unknown regulatory elements using probabilistic  ...  INCLUSive is a suite of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.  ...  This way, the user is spared the burden of retrieving all this relevant background information manually.  ... 
doi:10.1093/nar/gkg615 pmid:12824346 pmcid:PMC169021 fatcat:tw5vuw6zsffzfkfyozvtbf2o3i

Supporting System for Detecting Pathologies [chapter]

Carolina Zato, Juan F. De Paz, Fernando de la Prieta, Beatriz Martín
2011 Lecture Notes in Computer Science  
segmented data, a visual analysis of the information is carried out for the selection of relevant segments.  ...  Detecting these mutations allows to carry out diagnoses and to complete studies of sequencing in relevant regions of the DNA.  ...  Exploratory analysis of this data is crucial in helping to understand the data and to help form biological hypotheses.  ... 
doi:10.1007/978-3-642-21498-1_84 fatcat:fvrtrsjwyzgo3jpogxpnz2rooe

Integrating semantic transcriptomic data analysis and knowledge extraction from biological literature

Vid Podpecan, Dragana Miljkovic, Marko Petek, Tjasa Stare, Kristina Gruden, Igor Mozetic, Nada Lavrac
2013 2013 IEEE International Conference on Bioinformatics and Biomedicine  
We have integrated a methodology for semantic analysis of transcriptomic data, a system for automated extraction of biological relations from the literature, and a number of supporting components.  ...  The aim of the proposed approach is to give insight into the discovered patterns, help explaining the observed phenomena, enable the creation of new research hypotheses and assist in design of new experiments  ...  Section III discusses the results of the experiments, their evaluation and biological interpretation.  ... 
doi:10.1109/bibm.2013.6732540 dblp:conf/bibm/PodpecanMPSGML13 fatcat:s5e77i2lmzaite53apx5js36oi

Methods and Trends in Information Retrieval in Big Data Genomic Research

2019 VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE  
This paper presented the recent research trends, survey, reviews, experiments, and concepts in information retrieval applied to text, images and object features in big data genomic research.  ...  This paper described information retrieval (IR) and the common methods of finding, extracting, and mining information in genomic research through text mining, and natural language processing (NLP).  ...  The functional analysis of key biological processes and functions methods [44] were used in gene information retrieval.  ... 
doi:10.35940/ijitee.i1109.0789s219 fatcat:j2uramagd5a75jusrcor75w7ue

Practical Approaches to Analyzing Results of Microarray Experiments

Naftali Kaminski, Nir Friedman
2002 American Journal of Respiratory Cell and Molecular Biology  
We also deal with the problem of adding biologic meaning to the results of microarray experiments and describe advanced tools that represent different but valid directions in providing automated solutions  ...  The tools and approaches described and discussed here should provide the reader with a preliminary understanding of the analysis of the results of microarray experiments.  ...  Acknowledgments: Many of the ideas described in this paper were developed in collaboration with Amir Ben-Dor and Zohar Yakhini. The authors thank them for many useful and insightful discussions.  ... 
doi:10.1165/ajrcmb.27.2.f247 pmid:12151303 fatcat:fq6tvmh5kbet3jnb7ikeswxfze

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.  ...  WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or  ...  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

Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology

Hannah J Tipney, Sonia M Leach, Weiguo Feng, Richard Spritz, Trevor Williams, Lawrence Hunter
2009 BMC Bioinformatics  
In response to the frequently overwhelming output of high-throughput microarray experiments, we propose a methodology to facilitate interpretation of biological data in the context of existing knowledge  ...  Through the probabilistic integration of explicit and implicit data sources a functional interaction network can be constructed.  ...  The ultimate goal of any microarray experiment is to gain insight into the workings of cellular organisms by understanding the interactions of genes and proteins.  ... 
doi:10.1186/1471-2105-10-s2-s12 pmid:19208187 pmcid:PMC2646237 fatcat:zemzg6wvj5fcbf6hvgjrzurnge

An architecture for biological information extraction and representation

Aditya Vailaya, Peter Bluvas, Robert Kincaid, Allan Kuchinsky, Michael Creech, Annette Adler
2004 Proceedings of the 2004 ACM symposium on Applied computing - SAC '04  
We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation.  ...  In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation  ...  ACKNOWLEDGMENTS The authors thank David Moh and Christian LeCocq for their inputs in the design of the ALFA Object Model, and Will Old and Christian LeCocq for valuable discussions in defining the base  ... 
doi:10.1145/967900.967924 dblp:conf/sac/VailayaBKKCA04 fatcat:edvbqdifgnhzbbcduca4s5eiqu
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