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TXTGate: profiling gene groups with text-based information

Patrick Glenisson, Bert Coessens, Steven Van Vooren, Janick Mathys, Yves Moreau, Bart De Moor
2004 Genome Biology  
We implemented a framework called TXTGate that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes.  ...  By means of tailored vocabularies, term- as well as gene-centric views are offered on selected textual fields and MEDLINE abstracts used in LocusLink and the Saccharomyces Genome Database.  ...  Construction of domain vocabularies We constructed five different term-centric domain vocabularies that provide different views on the gene-specific information we indexed.  ... 
doi:10.1186/gb-2004-5-6-r43 pmid:15186494 pmcid:PMC463076 fatcat:iijxrcxvr5hffkpfnpwl4hbhvq

A Knowledge Integration Framework for Information Visualization [chapter]

Jinwook Seo, Ben Shneiderman
2005 Lecture Notes in Computer Science  
Our examples present hierarchical clustering of gene expression data, coordinated with a parallel coordinates view and with the gene annotation and gene ontology.  ...  The novel parallel coordinates view [6] powered by a direct-manipulation search, offers strong advantages, but requires some training for most users.  ...  Acknowledgements: We appreciate the support from and partnership with Eric Hoffman and his lab at the Children's National Medical Center, through NIH grant N01-NS-1-2339.  ... 
doi:10.1007/978-3-540-31842-2_21 fatcat:57qn7n4pyna3xhxqvpu6zugz2u

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

Nodin Weddington, Alexander Stuy, Ichiro Hiratani, Tyrone Ryba, Tomoki Yokochi, David M Gilbert
2008 BMC Bioinformatics  
These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property  ...  of specific cell types.  ...  ReplicationDomain will provide a valuable resource to consolidate replication profiles, making them more accessible to view and identify cell-type specific properties.  ... 
doi:10.1186/1471-2105-9-530 pmid:19077204 pmcid:PMC2636809 fatcat:ahd4afbvwjdwba3sxsgvwysyia

Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

R. K. Yadav, T. Girke, S. Pasala, M. Xie, G. V. Reddy
2009 Proceedings of the National Academy of Sciences of the United States of America  
The cell sample-specific gene expression profiling has resulted in a highresolution gene expression map to reveal gene expression networks specific to individual spatial domains of SAMs.  ...  The expression profiling of transcripts from 4 different cell populations and informatics analysis has revealed gene expression networks specific to different spatial domains of the stem cell niche.  ...  We thank Barbara Walter (Institute of Inegrative Genome Biology, University of California, Riverside) for help with the FACS sorting and microarray hybridizations, Zhenhua Deng for help with qRT-PCR analysis  ... 
doi:10.1073/pnas.0900843106 pmid:19258454 pmcid:PMC2660727 fatcat:7ilpulwzwbggdnwqqtvkamp5jq

An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

Wei Yu, Ajay Yesupriya, Anja Wulf, Junfeng Qu, Muin J Khoury, Marta Gwinn
2007 BMC Bioinformatics  
Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields.  ...  We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base.  ...  Acknowledgements Disclaimer: The findings and conclusions in this report are those of the author(s) and do not necessarily represent the views of CDC  ... 
doi:10.1186/1471-2105-8-436 pmid:17996092 pmcid:PMC2248211 fatcat:pvrufqedxjaurlr6gkratapkvi

The Human Epigenome Browser at Washington University

Xin Zhou, Brett Maricque, Mingchao Xie, Daofeng Li, Vasavi Sundaram, Eric A Martin, Brian C Koebbe, Cydney Nielsen, Martin Hirst, Peggy Farnham, Robert M Kuhn, Jingchun Zhu (+6 others)
2011 Nature Methods  
Investigators can also toggle between heatmap views and typical track-based, 'wiggle' views ( Supplementary Fig. 1 ).  ...  In differentiated cells, however, H3K4me3 or H3K27me3 signals are selectively lost, consistent with keeping some developmental genes on and others off in specific cell types.  ... 
doi:10.1038/nmeth.1772 pmid:22127213 pmcid:PMC3552640 fatcat:xwto33grm5hgfpy5qswc2kb56q

Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining

Shi Yu, Steven Van Vooren, Leon-Charles Tranchevent, Bart De Moor, Yves Moreau
2008 Computer applications in the biosciences : CABIOS  
We indexed 288 177 MEDLINE titles and abstracts with the TXTGate text profiling system and adapted the benchmark dataset of the Endeavour gene prioritization system that consists of 618 disease-causing  ...  Results: We investigated 5 different domain vocabularies, 2 text representation schemes and 27 linear ranking algorithms for disease gene prioritization by text mining.  ...  Comparison of prioritization performance using text profiles based on random vocabularies, domain vocabularies and no vocabulary.  ... 
doi:10.1093/bioinformatics/btn291 pmid:18689812 fatcat:6osfcq6xlzb3fiulgl2s6q2yvu

Gene prioritization and clustering by multi-view text mining

Shi Yu, Leon-Charles Tranchevent, Bart De Moor, Yves Moreau
2010 BMC Bioinformatics  
In such case, multi-view text mining is a superior and promising strategy for text-based disease gene identification.  ...  These controlled vocabularies are selected on the basis of nine well-known bio-ontologies and are applied to index the vast amounts of gene-based free-text information available in the MEDLINE repository  ...  SY performed text mining, programmed the algorithms, analyzed the data and wrote the paper.  ... 
doi:10.1186/1471-2105-11-28 pmid:20074336 pmcid:PMC3098068 fatcat:rja5rhssdrcsxd4xxsosux7sjq

FuncBase : a resource for quantitative gene function annotation

J. E. Beaver, M. Tasan, F. D. Gibbons, W. Tian, T. R. Hughes, F. P. Roth
2010 Bioinformatics  
FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations.  ...  Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system.  ...  View supporting evidence: Users may wish to further filter quantitative annotations based on their domain knowledge. Therefore, FuncBase displays key pieces of evidence underlying annotations.  ... 
doi:10.1093/bioinformatics/btq265 pmid:20495000 pmcid:PMC2894510 fatcat:q5wm5rewxjfp5h2v7aod4qkvoy

The MiST2 database: a comprehensive genomics resource on microbial signal transduction

Luke E. Ulrich, Igor B. Zhulin
2009 Nucleic Acids Research  
These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction.  ...  models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern  ...  Updated signaling profile collection All signal transduction proteins are identified based on the presence and/or absence of specific signaling domain profiles.  ... 
doi:10.1093/nar/gkp940 pmid:19900966 pmcid:PMC2808908 fatcat:qot3dwpmcfamxk7hm2x4wu37jm

PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya

Graham L. Cromar, Anthony Zhao, Xuejian Xiong, Lakshmipuram S. Swapna, Noeleen Loughran, Hongyan Song, John Parkinson
2016 Database: The Journal of Biological Databases and Curation  
These are designed to allow the user to identify and compare proteins with similar domain architectures across species and thus develop hypotheses about the evolution of lineage-specific trajectories.  ...  Among the existing tools available for phylogenetic profiles, PhyloPro provides several innovative domain-based features including a novel domain adjacency visualization tool.  ...  By design, all domain-based views use the longest peptide for the corresponding gene as the basis for domain comparisons.  ... 
doi:10.1093/database/baw013 pmid:26980519 pmcid:PMC4792532 fatcat:ijtm26q6cna37ifdxgmi47ouy4

Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers

J. Grilli, M. Romano, F. Bassetti, M. Cosentino Lagomarsino
2014 Nucleic Acids Research  
The families that are not captured by the model show abundance profiles that are markedly peaked around a mean value, possibly because of specific abundance selection.  ...  Based on these results, we define an abundance variability index that captures a family's evolutionary behavior (and thus some of its relevant functional properties) purely based on its cross-species abundance  ...  We converted the gene-based data into domains using the simple criterion that all domains belonging to transferred or duplicate genes are scored as transferred or duplicate domains.  ... 
doi:10.1093/nar/gku378 pmid:24829449 pmcid:PMC4066789 fatcat:s3ld35na5vdftgmya2wpiyl4vy

Parallel integration of heterogeneous genome-wide data sources

Derek Greene, Kenneth Bryan, Padraig Cunningham
2008 2008 8th IEEE International Conference on BioInformatics and BioEngineering  
Each source provides a distinct "view" of the same domain, but potentially encodes different biologically-relevant patterns.  ...  The resulting model preserves patterns that are unique to individual views, as well as those common to all views.  ...  The authors considered the application of each combination strategy with SVMs to learn gene functional classes from gene expression and phylogenetic profiles.  ... 
doi:10.1109/bibe.2008.4696710 dblp:conf/bibe/GreeneBC08 fatcat:5xvyztmhbzeyvj5v7pql6w6xgi

Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features

J R Semeiks, A Rizki, M J Bissell, I S Mian
2006 BMC Bioinformatics  
Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins.  ...  data pertaining to them that are present in text-based, gene-centered corpora.  ...  specific domain subfamily represented in the MYOEPITHELIAL gene list.  ... 
doi:10.1186/1471-2105-7-147 pmid:16542449 pmcid:PMC1435935 fatcat:dl2rp6dnq5cwti5bdaorkstgnu

Text Mining in Cancer Gene and Pathway Prioritization

Yuan Luo, Gregory Riedlinger, Peter Szolovits
2014 Cancer Informatics  
This review places existing gene prioritization tools against the backdrop of an integrative Omic hierarchy view toward cancer and focuses on the analysis of their text mining components.  ...  domains, protein interactions, and pathways.  ...  PSZ contributed to the analysis and categorization of text mining methods in gene and pathway prioritization. All authors reviewed and approved of the final manuscript.  ... 
doi:10.4137/cin.s13874 pmid:25392685 pmcid:PMC4216063 fatcat:mtk6jnyvxjbntedeioojlmrq3u
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