ViBrism DB
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ViBrism DB is a database for anatomical gene expression maps and topological co-expression network graphs created with original techniques of microtomy-based gene expression measurements, Transcriptome Tomography. The DB is equipped with a WebGL-based 2D/3D visualization platform, BAH viewer, and a network viewer. Users can access a total of 172,022 datasets of coding/non-coding transcripts and lncRNAs, present in the mouse brains at four post-natal stages. Expression maps are seen in the whole anatomical context of 3D MR images of the brains. In situ hybridization images and anatomical area maps are browsable in the same space of 3D expression maps. Created images are shareable using URLs, including scene-setting parameters. The DB is expandable by community activity.
Description
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ViBrism DB is a database for anatomical gene expression maps and topological co-expression network graphs created with original techniques of microtomy-based gene expression measurements, Transcriptome Tomography. The DB is equipped with a WebGL-based 2D/3D visualization platform, BAH viewer, and a network viewer. Users can access a total of 172,022 datasets of coding/non-coding transcripts and lncRNAs, present in the mouse brains at four post-natal stages. Expression maps are seen in the whole anatomical context of 3D MR images of the brains. In situ hybridization images and anatomical area maps are browsable in the same space of 3D expression maps. Created images are shareable using URLs, including scene-setting parameters. The DB is expandable by community activity.
metasource: Fairsharing.orgversion: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ViBrism DB (http://vibrism.neuroinf.jp/) is a database for anatomical gene expression maps and topological co-expression network graphs created with original techniques of microtomy-based gene expression measurements, Transcriptome Tomography. The DB is equipped with a WebGL-based 2D/3D visualization platform, BAH viewer, and a network viewer. Users can access a total of 172,022 datasets of coding/non-coding transcripts and lncRNAs, present in the mouse brains at four post-natal stages. Expression maps are seen in the whole anatomical context of 3D MR images of the brains. In situ hybridization images and anatomical area maps are browsable in the same space of 3D expression maps. Created images are shareable using URLs, including scene-setting parameters. The DB is expandable by community activity.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://vibrism.neuroinf.jp/Webpage
More detailed information about this field from each metasource.
http://vibrism.neuroinf.jp/
metasource: Fairsharing.orgversion: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
https://vibrism.neuroinf.jp/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by-sa/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Transcriptome tomography for brain analysis in the web-accessible anatomical space
PMID: 23028969
metasource: Fairsharing.org
version: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks
PMID: 30371824
metasource: Fairsharing.org
version: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain
PMID: 25382412
metasource: Fairsharing.org
version: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gky951
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Transcriptome tomography for brain analysis in the web-accessible anatomical space
PMID: 23028969
metasource: Fairsharing.org
version: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks
PMID: 30371824
metasource: Fairsharing.org
version: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain
PMID: 25382412
metasource: Fairsharing.org
version: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gky951
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Transcriptome tomography for brain analysis in the web-accessible anatomical space
PubMed citations: 10.
10 articles citing: Transcriptome tomography for brain analysis in the web-accessible anatomical space
Museum of spatial transcriptomics. PMID:35273392
Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data. PMID:35061216
Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology. PMID:32507771
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks. PMID:30371824
Post-transcriptional Processing of mRNA in Neurons: The Vestiges of the RNA World Drive Transcriptome Diversity. PMID:30210293
On the Usage of Brain Atlases in Neuroimaging Research. PMID:30094652
A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing. PMID:29507408
Site-specific gene expression analysis using an automated tissue micro-dissection punching system. PMID:28659603
Spatially resolved transcriptomics and beyond. PMID:25446315
Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain. PMID:25382412 -
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks
PubMed citations: 3.
3 articles citing: ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks
Digital Brain Maps and Virtual Neuroscience: An Emerging Role for Light-Sheet Fluorescence Microscopy in Drug Development. PMID:35516798
Tales from topographic oceans: topologically associated domains and cancer. PMID:31505466
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. PMID:30626175 -
Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain
PubMed citations: 2.
2 articles citing: Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks. PMID:30371824
Transcriptome of neonatal preBötzinger complex neurones in Dbx1 reporter mice. PMID:28819234 - http://dx.doi.org/10.1093/nar/gky951
Tags:
Tags
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gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
magnetic resonance imaging
metasource: Fairsharing.org
version: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
magnetic resonance imaging
metasource: Fairsharing.orgversion: FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
gene expression magnetic resonance imaging microarray data and other gene expression
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