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TXTGate: profiling gene groups with text-based information
2004
Genome Biology
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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]
2005
Lecture Notes in Computer Science
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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
2008
BMC Bioinformatics
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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
2009
Proceedings of the National Academy of Sciences of the United States of America
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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
2007
BMC Bioinformatics
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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
2011
Nature Methods
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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
2008
Computer applications in the biosciences : CABIOS
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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
2010
BMC Bioinformatics
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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
2010
Bioinformatics
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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
2009
Nucleic Acids Research
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2014
Nucleic Acids Research
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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
2008
2008 8th IEEE International Conference on BioInformatics and BioEngineering
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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
2006
BMC Bioinformatics
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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
2014
Cancer Informatics
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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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