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Analysis of multiplex gene expression maps obtained by voxelation

Li An, Hongbo Xie, Mark H Chin, Zoran Obradovic, Desmond J Smith, Vasileios Megalooikonomou
2009 BMC Bioinformatics  
, Xiaohua Hu and Yiming Chen S10 Analysis of multiplex gene expression maps obtained by voxelation Li An, Hongbo Xie, Mark H Chin, Zoran Obradovic, Desmond J Smith and Vasileios Megalooikonomou IEEE International  ...  Honavar S5 Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms Xiaotong Lin, Mei Liu and Xue-wen Chen S6 Modeling post-transcriptional regulation activity  ... 
doi:10.1186/1471-2105-10-s4-s10 pmid:19426449 pmcid:PMC2681070 fatcat:vpf7fb2ddjdqvl4qff2o766jzi

Analysis of Multiplex Gene Expression Maps Obtained by Voxelation

Li An, Hongbo Xie, Mark Chin, Zoran Obradovic, Desmond Smith, Vasileios Megalooikonomou
2008 2008 IEEE International Conference on Bioinformatics and Biomedicine  
Olivier Bodenreider from the US National Library of Medicine for assisting us in calculating the similarity values of pairwise GO terms  ...  average of gene expression maps of significant clusters obtained by k-means for different ontologies.  ...  Gene expression patterns obtained by voxelation show good agreement with the known expression patterns.  ... 
doi:10.1109/bibm.2008.67 dblp:conf/bibm/AnXCOSM08 fatcat:yakhrqdt6bfpbf5hvoq757heci

Learning pair-wise gene functional similarity by multiplex gene expression maps

Li An, Haibin Ling, Zoran Obradovic, Desmond J Smith, Vasileios Megalooikonomou
2012 BMC Bioinformatics  
However, not much work has considered the connection between gene functions and location of a gene's expression in the mammalian tissues.  ...  The relationships between the gene functional similarity and gene expression profile, and between gene function annotation and gene sequence have been studied extensively.  ...  Competing interests The authors declare that they have no significant competing financial, professional or personal interests that might have influenced the performance or presentation of the work described  ... 
doi:10.1186/1471-2105-13-s3-s1 pmid:22536893 pmcid:PMC3375633 fatcat:r3owbohgo5hhpnk2njkat6lwj4

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially-resolved RNA-seq

Sabrina Zechel, Pawel Zajac, Peter Lönnerberg, Carlos F Ibáñez, Sten Linnarsson
2014 Genome Biology  
Conclusions: We demonstrate that spatially resolved RNA-seq is ideally suited for high resolution topographical mapping of genome-wide gene expression in heterogeneous anatomical structures such as the  ...  Here, we combined laser-capture microdissection and multiplex RNA-sequencing to map the transcriptome of MGE cells at a spatial resolution of 50 μm.  ...  (A) Gene expression clusters obtained by Ayasdi analysis (each node representing one voxel).  ... 
doi:10.1186/preaccept-9143209091271531 pmid:25344199 pmcid:PMC4234883 fatcat:xzk5q5bgtnbf7dtb2voaxi3yya

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq

Sabrina Zechel, Pawel Zajac, Peter Lönnerberg, Carlos F Ibáñez, Sten Linnarsson
2014 Genome Biology  
Conclusions: We demonstrate that spatially resolved RNA-seq is ideally suited for high resolution topographical mapping of genome-wide gene expression in heterogeneous anatomical structures such as the  ...  Here, we combined laser-capture microdissection and multiplex RNA-sequencing to map the transcriptome of MGE cells at a spatial resolution of 50 μm.  ...  (A) Gene expression clusters obtained by Ayasdi analysis (each node representing one voxel).  ... 
doi:10.1186/s13059-014-0486-z pmid:25344199 pmcid:PMC4234883 fatcat:emcjbqgvtnbktlq2nqqxbozkzy

Identifying pair-wise gene functional similarity by multiplex gene expression maps and supervised learning

Li An, Haibin Ling, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou
2011 Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11  
Gene expression maps, which contain spatial information regarding the expression of genes in mice's brain, are obtained by combining voxelation and microarrays.  ...  By considering pairs of genes from an original dataset as samples whose features are extracted from expression maps and labels are the functional similarities of pairs of genes, we explore the relationship  ...  Gene expression patterns (maps) obtained by voxelation show good agreement with known expression patterns [12] .  ... 
doi:10.1145/2147805.2147825 dblp:conf/bcb/AnLOSM11 fatcat:wo3z4ybcvnhirbb3mj2zuwqixm

Genome scale mapping of brain gene expression

Ram P Singh, Desmond J Smith
2003 Biological Psychiatry  
Voxelation employs analysis of spatially registered cubes from the brain, whereas GET entails analysis of parallel slices obtained by rotation about multiple axes.  ...  Two new approaches, voxelation and gene expression tomography (GET), permit multiplex acquisition of gene expression patterns in the brain.  ...  For creation of high-quality expression maps of the mouse brain, linear RNA amplification techniques (Kacharmina et al 1999) should readily permit creation of multiplex gene expression maps of 300 voxels  ... 
doi:10.1016/s0006-3223(03)00238-5 pmid:12814858 fatcat:lman75dimbaqpllxcfjj7s4ete

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

Vikas Trivedi, Harry M. T. Choi, Scott E. Fraser, Niles A. Pierce
2018 Development  
As we demonstrate by examining gene circuits underlying somitogenesis, quantitative read-out and read-in analyses provide the strengths of flow cytometry expression analyses, but by preserving subcellular  ...  Gene expression can be queried in two directions: read-out from anatomical space to expression space reveals co-expression relationships in selected regions of the specimen; conversely, read-in from multidimensional  ...  The findings are those of the authors and should not be interpreted as representing the official views or policies of the U.S. Government.  ... 
doi:10.1242/dev.156869 pmid:29311262 fatcat:53r5qi7xhfabfebidiubrbscta

Multiplex Three-Dimensional Brain Gene Expression Mapping in a Mouse Model of Parkinson's Disease

V. M. Brown, A. Ossadtchi, A. H. Khan, S. Yee, G. Lacan, W. P. Melega, S. R. Cherry, R. M. Leahy, D. J. Smith
2002 Genome Research  
Spatially registered voxels (cubes) are analyzed, resulting in multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems.  ...  To facilitate high-throughput 3D imaging of brain gene expression, a new method called voxelation has been developed.  ...  The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gr.229002 pmid:12045141 pmcid:PMC1383741 fatcat:en7pjvfbgfcyhmuukqttpd6rzu

Multiplex Three-Dimensional Brain Gene Expression Mapping in a Mouse Model of Parkinson's Disease

V. M. Brown
2002 Genome Research  
Spatially registered voxels (cubes) are analyzed, resulting in multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems.  ...  To facilitate high-throughput 3D imaging of brain gene expression, a new method called voxelation has been developed.  ...  The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gr.229002. fatcat:cyagdalp6ndvvognoghiznfzrq

Dual spatial maps of transcript and protein abundance in the mouse brain

Christopher C Park, Vladislav A Petyuk, Wei-Jun Qian, Richard D Smith, Desmond J Smith
2009 Espert Review of Proteomics  
Highlighted are dual spatial maps of these molecules obtained using voxelation of the mouse brain.  ...  The mammalian brain is a complex organ exhibiting a rich variety of gene expression patterns across a broad range of cell types.  ...  Acknowledgments Financial & competing interests disclosure Portions of the research were supported by the NIH National Center for Research Resources (RR18522 to R.D.S.) and NIH grant R01 NS050148 to Desmond  ... 
doi:10.1586/epr.09.46 pmid:19489697 pmcid:PMC2744401 fatcat:ah6ckkw76remrdkoof7xbmi3im

High-Throughput Imaging of Brain Gene Expression

V. M. Brown
2002 Genome Research  
It employs high-throughput analysis of spatially registered voxels (cubes) to produce multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems.  ...  Voxelation is a new method for acquisition of three dimensional (3D) gene expression patterns in the brain.  ...  ACKNOWLEDGMENTS The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gr.204102 pmid:11827944 fatcat:r2cw2x7dyrf6jgtwm4vje5rfpa

Cell segmentation-free inference of cell types from in situ transcriptomics data

Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle (+2 others)
2021 Nature Communications  
We apply SSAM to three mouse brain tissue images: the somatosensory cortex imaged by osmFISH, the hypothalamic preoptic region by MERFISH, and the visual cortex by multiplexed smFISH.  ...  Here, we present a method called Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation (SSAM), a robust cell segmentation-free computational framework for identifying cell-types  ...  The preliminary analysis of multiplexed smFISH data occurred during the SpaceTx SpaceJam Hackathon at the Allen Institute for Brain Science, which was organized by Ed Lein, and generously supported by  ... 
doi:10.1038/s41467-021-23807-4 pmid:34112806 fatcat:dx65syjkxbbxno3libawc345ma

Segmentation-free inference of cell-types from in situ transcriptomics data [article]

Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Simone Codeluppi, Matthias Schlesner, Bosiljka Tasic, Roland Eils, Naveed Ishaque
2019 bioRxiv   pre-print
Here, we present a robust segmentation-free computational framework, applicable to a variety of in situ transcriptomics platforms, called Spot-based Spatial cell-type Analysis by Multidimensional mRNA  ...  We apply SSAM to three mouse brain tissue images: the somatosensory cortex imaged by osmFISH, the hypothalamic preoptic region by MERFISH, and the visual cortex by multiplexed smFISH.  ...  The preliminary analysis of multiplexed smFISH data occurred during the SpaceTx SpaceJam Hackathon at the Allen Institute for Brain Science, which was organized by Ed Lein, and generously supported by  ... 
doi:10.1101/800748 fatcat:h3hquog3gjgefdrn7ycfwa543u

When Bigger Is Better: 3D RNA Profiling of the Developing Head in the Catshark Scyliorhinus canicula

Hélène Mayeur, Maxence Lanoizelet, Aurélie Quillien, Arnaud Menuet, Léo Michel, Kyle John Martin, Sébastien Dejean, Patrick Blader, Sylvie Mazan, Ronan Lagadec
2021 Frontiers in Cell and Developmental Biology  
continuity genome recently released in the catshark, and projected read counts onto a digital model of the head obtained by confocal microscopy.  ...  This results in the generation of a genome-wide 3D atlas, containing expression data for most protein-coding genes in a digital model of the embryonic head.  ...  For the bioinformatic analysis, reads were demultiplexed and mapped onto a gene reference obtained taking advantage of the catshark genome NCBI annotation and of transcriptomic resources available in our  ... 
doi:10.3389/fcell.2021.744982 pmid:34746140 pmcid:PMC8569936 fatcat:xq7hpjldhvdfhm4rwqfgq6uc3e
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