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A Geometric Database for Gene Expression Data
[article]
2003
Symposium on geometry processing : [proceedings]. Symposium on Geometry Processing
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In this paper, we describe the structure of a geometric database for the mouse brain that allows biologists to organize and search this gene expression data. ...
New gene expression images are added to the database by deforming this atlas onto each image using techniques developed for fitting subdivision surfaces to scatter data. ...
Acknowledgement This work is supported in part by a training fellowship from the W.M. Keck Foundation to the Gulf Coast Consortia through the Keck Center for Computational and Structural Biology. ...
doi:10.2312/sgp/sgp03/166-176
fatcat:6q43buhtrrff7mwncrgxlgzimu
A geometric database for gene expression data
2003
Symposium on geometry processing : [proceedings]. Symposium on Geometry Processing
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In this paper, we describe the structure of a geometric database for the mouse brain that allows biologists to organize and search this gene expression data. ...
New gene expression images are added to the database by deforming this atlas onto each image using techniques developed for fitting subdivision surfaces to scatter data. ...
Acknowledgement This work is supported in part by a training fellowship from the W.M. Keck Foundation to the Gulf Coast Consortia through the Keck Center for Computational and Structural Biology. ...
pmid:20631855
pmcid:PMC2903551
fatcat:habsunpesngpjcpgyfggqoq2cq
Recovering key biological constituents through sparse representation of gene expression
2011
Computer applications in the biosciences : CABIOS
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We suggest that the geometrical approach presented here is suitable for a broad range of high-dimensional experimental data. ...
Specifically, we find, for the expression profile of each particular gene, its approximation as a linear combination of profiles of a few other genes. ...
In this study, we applied a different approach to gene expression data analysis. ...
doi:10.1093/bioinformatics/btr002
pmid:21258061
fatcat:gt5ghbuf5rhffgbbiqhwzfrp4m
The contribution of cell cycle to heterogeneity in single-cell RNA-seq data
2016
Nature Biotechnology
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This approach has a long record of successful application in gene expression experiments 5 . ...
Using principal component analysis (PCA), we found that the first principal component (PC1) tracked the geometric library size (R 2 > 0.99) -the sum of log expression values over all genes in a cell -and ...
doi:10.1038/nbt.3498
pmid:27281413
pmcid:PMC5934759
fatcat:5utywwmmzjdhjdm5p4kra3dmrq
3-D Reconstructions for graphical databases of gene expression
1997
Seminars in Cell and Developmental Biology
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Modern techniques in molecular biology are providing a great deal of information about the genetic control of embryo development, particularly about the patterns of gene expression. ...
Here, we discuss methods for reconstructing such data from serial sections of tissues and discuss approaches to aligning adjacent sections, removing sectioning distortions and delineating the final patterns ...
Acknowledgements The work has been part of the European Science Foundation Network on 'Embryological Databases' whom we thank for funding this collaboration. ...
doi:10.1006/scdb.1997.0175
pmid:9441955
fatcat:5dwndefdefgynjik34yjjuqexu
Application of Sparse Representation in Bioinformatics
2021
Frontiers in Genetics
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expression profiles, and an introduction to related cancers and gene expression profile database. ...
Inspired by L1-norm minimization methods, such as basis pursuit, compressed sensing, and Lasso feature selection, in recent years, sparse representation shows up as a novel and potent data processing method ...
ACKNOWLEDGMENTS We thank Maxine Garcia, PhD, from Liwen Bianji (Edanz) (www. liwenbianji.cn/) for editing the English text of a draft of this manuscript. ...
doi:10.3389/fgene.2021.810875
pmid:34976030
pmcid:PMC8715914
fatcat:fgioonmcffd7bftmvpoghbqucy
Reverse deduction of virtual chromosomes of manufactured products for their gene-engineering-based innovative design
2005
Computer-Aided Design
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With the similarity between living beings' evolution and manufactured products' development, gene-engineering techniques have been applied to develop a bionic design theory and methodology for product ...
This paper introduces the gene-engineering-based innovative design method, and discloses the contents and data structure of products' chromosomes and applies database techniques to edit and store products ...
Database structure for products' chromosomes
Main framework of databases for products' chromosomes The product's chromosome contains so much information, and is so complicated in data structure, that ...
doi:10.1016/j.cad.2005.02.009
fatcat:mdba27bvmvgkpfhhwoxugraeue
Human gene expression sensitivity according to large scale meta-analysis
2009
BMC Bioinformatics
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Ohn et al. first studied this gene property with yeast transcriptional profiling data. Results: Here we propose a calculation framework for gene expression sensitivity analysis. ...
of combining the gene expression sensitivity in the microarray analysis. ...
Acknowledgements We would like to thank Xiaojing Wang, Yao Yu and Yun Li for helpful dis- ...
doi:10.1186/1471-2105-10-s1-s56
pmid:19208159
pmcid:PMC2648786
fatcat:3bbxzamrvjdfbj3ccjs6ilzzla
Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR
2011
BMC Molecular Biology
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Transcriptomic data normalized by the geometric average of these three genes demonstrated that genes of the lycopene synthetic pathway maintained steady expression upon enzyme overexpression. ...
The objective of this study is to identify a set of reliable reference genes for transcription analysis in recombinant protein over-expression studies in E. coli. ...
To identify suitable candidate genes, we surveyed five major microarray databases (Many Microbe Database M 3D , NIH-GEO, Stanford Microarray Database, ExpressDB and Array Express) for projects pertinent ...
doi:10.1186/1471-2199-12-18
pmid:21513543
pmcid:PMC3110127
fatcat:d7ytw4dr5jag7cb6tcygffwkk4
Cytotoxic Effect of RecombinantMycobacterium tuberculosisCFP-10/ESAT-6 Protein on the Crucial Pathways of WI-38 Cells
2009
Journal of Biomedicine and Biotechnology
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To unravel the cytotoxic effect of the recombinant CFP-10/ESAT-6 protein (rCFES) on WI-38 cells, an integrative analysis approach, combining time-course microarray data and annotated pathway databases, ...
The potentially crucial pathways were selected based on a composite criterion characterizing the average significance and topological properties of important genes. ...
To validate the microarray data, real-time qRT-PCR using SYBR Green I Kit (Roche) was performed to assess RNA expression level accuracy. A set of important genes were selected for qRT-PCR assessment. ...
doi:10.1155/2009/917084
pmid:19584916
pmcid:PMC2702506
fatcat:tuugq4mui5hmfh6um4yskr7y6a
Genic insights from integrated human proteomics in GeneCards
2016
Database: The Journal of Biological Databases and Curation
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GeneCards is a one-stop shop for searchable human gene annotations ...
Acknowledgements We thank Gil Stelzer and Omer Markovitch for helpful discussions. Conflict of interest. None declared. ...
GeneCards, the human gene compendium, is a genecentric database integrating data for 152 704 human genes from 125 sources (11) . ...
doi:10.1093/database/baw030
pmid:27048349
pmcid:PMC4820835
fatcat:o2qmsm6l2ve7bpyvhbj2pnu6re
RgS-Miner: A Biological Data Warehousing, Analyzing and Mining System for Identifying Transcriptional Regulatory Sites in Human Genome
[chapter]
2004
Lecture Notes in Computer Science
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Recently, biological databases and analytical methods have become available for analyzing gene expression and transcriptional regulatory sequences. ...
Beyond methods for predicting transcriptional regulatory sites, new automated and integrated methods for analyzing gene upstream sequences on a higher level are urgently required. ...
Yu-Chung Chang are appreciated for their valuable discussions regarding molecular biology. We also thank Prof. Cheng-Yan Kao for his valuable suggestions and comments. ...
doi:10.1007/978-3-540-30075-5_72
fatcat:lnntr6t64rf6hdzyzplubuwpbe
A study of alternative splicing in the pig
2010
BMC Research Notes
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Six genes were shown to have tissue specific alternatively spliced transcripts with expression patterns matching those of the EST data. ...
Expressed sequence tags (ESTs) provide evidence of a great number of possible alternative isoforms. ...
Acknowledgements The authors thank Minna Jakobsen for excellent technical assistance and Karsten Sceibye-Alsing for bioinformatic assistance. ...
doi:10.1186/1756-0500-3-123
pmid:20444244
pmcid:PMC2882375
fatcat:qsuihl6manb5djgxl7lljer7oq
A NEW STRATEGY OF GEOMETRICAL BICLUSTERING FOR MICROARRAY DATA ANALYSIS
2007
Proceedings of the 5th Asia-Pacific Bioinformatics Conference
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In this paper, we present a new biclustering algorithm to provide the geometrical interpretation of similar microarray gene expression profiles. ...
Furthermore, we have applied it to a large database of gene expression profiles of multiple human organs and the resulting biclusters show clear biological meanings. ...
Applications We apply our algorithm to the gene expression database of multiple human organs [13] . ...
doi:10.1142/9781860947995_0008
fatcat:edyoj4s3szeg7otsx3v2ngtxpq
Biclustering gene expression data based on a high dimensional geometric method
2005
2005 International Conference on Machine Learning and Cybernetics
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In gene expression data, a bicluster is a subset of genes exhibiting a consistent pattern over a subset of the conditions. ...
In this paper, we propose a new method to detect biclusters in gene expression data. ...
Acknowledgements The work described in this paper was fully supported by an interdisciplinary grant (Project 9010003) and a strategic research grant (Project 7001706) from City University of Hong Kong. ...
doi:10.1109/icmlc.2005.1527527
fatcat:vorxumwctbesteln2wrkbsiola
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