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A Geometric Database for Gene Expression Data [article]

Tao Ju, Joe Warren, Gregor Eichele, Christina Thaller, Wah Chiu, James Carson
2003 Symposium on geometry processing : [proceedings]. Symposium on Geometry Processing  
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

Tao Ju, Joe Warren, Gregor Eichele, Christina Thaller, Wah Chiu, James Carson
2003 Symposium on geometry processing : [proceedings]. Symposium on Geometry Processing  
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

Yosef Prat, Menachem Fromer, Nathan Linial, Michal Linial
2011 Computer applications in the biosciences : CABIOS  
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

Andrew McDavid, Greg Finak, Raphael Gottardo
2016 Nature Biotechnology  
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

R.A. Baldock, F.J. Verbeek, J-L. Vonesch
1997 Seminars in Cell and Developmental Biology  
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

Shuguang Han, Ning Wang, Yuxin Guo, Furong Tang, Lei Xu, Ying Ju, Lei Shi
2021 Frontiers in Genetics  
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

Ke-Zhang Chen, Xin-An Feng, Xiao-Chuan Chen
2005 Computer-Aided Design  
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

Pei Hao, Siyuan Zheng, Jie Ping, Kang Tu, Christian Gieger, Rui Wang-Sattler, Yang Zhong, Yixue Li
2009 BMC Bioinformatics  
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

Kang Zhou, Lihan Zhou, Qing Lim, Ruiyang Zou, Gregory Stephanopoulos, Heng-Phon Too
2011 BMC Molecular Biology  
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

Kun-Nan Tsai, Err-Cheng Chan, Tsung-Yeh Tsai, Kuei-Tien Chen, Chun-Yu Chen, Kenneth Hung, Chung-Ming Chen
2009 Journal of Biomedicine and Biotechnology  
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

Simon Fishilevich, Shahar Zimmerman, Asher Kohn, Tsippi Iny Stein, Tsviya Olender, Eugene Kolker, Marilyn Safran, Doron Lancet
2016 Database: The Journal of Biological Databases and Curation  
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]

Yi-Ming Sun, Hsien-Da Huang, Jorng-Tzong Horng, Shir-Ly Huang, Ann-Ping Tsou
2004 Lecture Notes in Computer Science  
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

Ann-Britt Nygard, Susanna Cirera, Michael J Gilchrist, Jan Gorodkin, Claus B Jørgensen, Merete Fredholm
2010 BMC Research Notes  
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

HONGYA ZHAO, ALAN W. C. LIEW, HONG YAN
2007 Proceedings of the 5th Asia-Pacific Bioinformatics Conference  
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

Xiang-Chao Gan, Alan Wee-Chung Liew, Hong Yan
2005 2005 International Conference on Machine Learning and Cybernetics  
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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