brainspace Search Results


brainspan atlas dataset  (Allen Institute for Brain Science)
90
Allen Institute for Brain Science brainspan atlas dataset
Gene Ontology (GO) annotation was used to identify gene classes containing an overrepresentation of genes that were differentially expressed between day 0 and day 4 in iNGN cells. The majority of GO terms with an overrepresentation of downregulated genes (green) are related to cell cycle and nucleic acid metabolism, while GO terms with many upregulated genes (purple) include classes related to neuron development and physiology. For example, most genes in the Gene Ontology classification of ‘regulation of neurogenesis’ (inset) including neural progenitor markers are significantly upregulated as shown in the heatmap. RNA-Seq data of uninduced iNGN (day 0, blue) and iNGN cells (day 4, black) are compared to the Allen <t>BrainSpan</t> data, by computing the Pearson's correlation coefficients between the iNGN cells and all brain samples at each developmental time point. This shows that iNGN gene expression is more consistent with prenatal brain gene expression, and the correlation is significantly higher for day 4 iNGN cells, compared to day 0 cells (one-sided two-sample t -test, with P -values shown in red dots). Pearson's correlation coefficients were subsequently computed between day 4 iNGN cells and profiles for brain regions at each time point. The 500 most highly upregulated genes in day 4 iNGN cells were used as a neuronal signature. At each time point, Z-scores were computed for each brain region to assess their relative similarity to the iNGN signature, in comparison with the remaining brain regions. This demonstrated less similarity of iNGN cells to cortical brain structures and indicated higher similarities to the mediodorsal nucleus of thalamus, amygdaloid complex, hippocampus and cerebellar cortex. Pcw, postconception weeks.
Brainspan Atlas Dataset, supplied by Allen Institute for Brain Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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matlab toolbox for brainspace  (MathWorks Inc)
96
MathWorks Inc matlab toolbox for brainspace
Gene Ontology (GO) annotation was used to identify gene classes containing an overrepresentation of genes that were differentially expressed between day 0 and day 4 in iNGN cells. The majority of GO terms with an overrepresentation of downregulated genes (green) are related to cell cycle and nucleic acid metabolism, while GO terms with many upregulated genes (purple) include classes related to neuron development and physiology. For example, most genes in the Gene Ontology classification of ‘regulation of neurogenesis’ (inset) including neural progenitor markers are significantly upregulated as shown in the heatmap. RNA-Seq data of uninduced iNGN (day 0, blue) and iNGN cells (day 4, black) are compared to the Allen <t>BrainSpan</t> data, by computing the Pearson's correlation coefficients between the iNGN cells and all brain samples at each developmental time point. This shows that iNGN gene expression is more consistent with prenatal brain gene expression, and the correlation is significantly higher for day 4 iNGN cells, compared to day 0 cells (one-sided two-sample t -test, with P -values shown in red dots). Pearson's correlation coefficients were subsequently computed between day 4 iNGN cells and profiles for brain regions at each time point. The 500 most highly upregulated genes in day 4 iNGN cells were used as a neuronal signature. At each time point, Z-scores were computed for each brain region to assess their relative similarity to the iNGN signature, in comparison with the remaining brain regions. This demonstrated less similarity of iNGN cells to cortical brain structures and indicated higher similarities to the mediodorsal nucleus of thalamus, amygdaloid complex, hippocampus and cerebellar cortex. Pcw, postconception weeks.
Matlab Toolbox For Brainspace, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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matlab toolbox for brainspace - by Bioz Stars, 2026-06
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brainspace  (MathWorks Inc)
96
MathWorks Inc brainspace
Gene Ontology (GO) annotation was used to identify gene classes containing an overrepresentation of genes that were differentially expressed between day 0 and day 4 in iNGN cells. The majority of GO terms with an overrepresentation of downregulated genes (green) are related to cell cycle and nucleic acid metabolism, while GO terms with many upregulated genes (purple) include classes related to neuron development and physiology. For example, most genes in the Gene Ontology classification of ‘regulation of neurogenesis’ (inset) including neural progenitor markers are significantly upregulated as shown in the heatmap. RNA-Seq data of uninduced iNGN (day 0, blue) and iNGN cells (day 4, black) are compared to the Allen <t>BrainSpan</t> data, by computing the Pearson's correlation coefficients between the iNGN cells and all brain samples at each developmental time point. This shows that iNGN gene expression is more consistent with prenatal brain gene expression, and the correlation is significantly higher for day 4 iNGN cells, compared to day 0 cells (one-sided two-sample t -test, with P -values shown in red dots). Pearson's correlation coefficients were subsequently computed between day 4 iNGN cells and profiles for brain regions at each time point. The 500 most highly upregulated genes in day 4 iNGN cells were used as a neuronal signature. At each time point, Z-scores were computed for each brain region to assess their relative similarity to the iNGN signature, in comparison with the remaining brain regions. This demonstrated less similarity of iNGN cells to cortical brain structures and indicated higher similarities to the mediodorsal nucleus of thalamus, amygdaloid complex, hippocampus and cerebellar cortex. Pcw, postconception weeks.
Brainspace, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/brainspace/product/MathWorks Inc
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brainspace - by Bioz Stars, 2026-06
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brainspan  (BrainScope)
90
BrainScope brainspan
Gene Ontology (GO) annotation was used to identify gene classes containing an overrepresentation of genes that were differentially expressed between day 0 and day 4 in iNGN cells. The majority of GO terms with an overrepresentation of downregulated genes (green) are related to cell cycle and nucleic acid metabolism, while GO terms with many upregulated genes (purple) include classes related to neuron development and physiology. For example, most genes in the Gene Ontology classification of ‘regulation of neurogenesis’ (inset) including neural progenitor markers are significantly upregulated as shown in the heatmap. RNA-Seq data of uninduced iNGN (day 0, blue) and iNGN cells (day 4, black) are compared to the Allen <t>BrainSpan</t> data, by computing the Pearson's correlation coefficients between the iNGN cells and all brain samples at each developmental time point. This shows that iNGN gene expression is more consistent with prenatal brain gene expression, and the correlation is significantly higher for day 4 iNGN cells, compared to day 0 cells (one-sided two-sample t -test, with P -values shown in red dots). Pearson's correlation coefficients were subsequently computed between day 4 iNGN cells and profiles for brain regions at each time point. The 500 most highly upregulated genes in day 4 iNGN cells were used as a neuronal signature. At each time point, Z-scores were computed for each brain region to assess their relative similarity to the iNGN signature, in comparison with the remaining brain regions. This demonstrated less similarity of iNGN cells to cortical brain structures and indicated higher similarities to the mediodorsal nucleus of thalamus, amygdaloid complex, hippocampus and cerebellar cortex. Pcw, postconception weeks.
Brainspan, supplied by BrainScope, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 90 stars, based on 1 article reviews
brainspan - by Bioz Stars, 2026-06
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open source toolbox brainspace  (MathWorks Inc)
96
MathWorks Inc open source toolbox brainspace
Gene Ontology (GO) annotation was used to identify gene classes containing an overrepresentation of genes that were differentially expressed between day 0 and day 4 in iNGN cells. The majority of GO terms with an overrepresentation of downregulated genes (green) are related to cell cycle and nucleic acid metabolism, while GO terms with many upregulated genes (purple) include classes related to neuron development and physiology. For example, most genes in the Gene Ontology classification of ‘regulation of neurogenesis’ (inset) including neural progenitor markers are significantly upregulated as shown in the heatmap. RNA-Seq data of uninduced iNGN (day 0, blue) and iNGN cells (day 4, black) are compared to the Allen <t>BrainSpan</t> data, by computing the Pearson's correlation coefficients between the iNGN cells and all brain samples at each developmental time point. This shows that iNGN gene expression is more consistent with prenatal brain gene expression, and the correlation is significantly higher for day 4 iNGN cells, compared to day 0 cells (one-sided two-sample t -test, with P -values shown in red dots). Pearson's correlation coefficients were subsequently computed between day 4 iNGN cells and profiles for brain regions at each time point. The 500 most highly upregulated genes in day 4 iNGN cells were used as a neuronal signature. At each time point, Z-scores were computed for each brain region to assess their relative similarity to the iNGN signature, in comparison with the remaining brain regions. This demonstrated less similarity of iNGN cells to cortical brain structures and indicated higher similarities to the mediodorsal nucleus of thalamus, amygdaloid complex, hippocampus and cerebellar cortex. Pcw, postconception weeks.
Open Source Toolbox Brainspace, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/open source toolbox brainspace/product/MathWorks Inc
Average 96 stars, based on 1 article reviews
open source toolbox brainspace - by Bioz Stars, 2026-06
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brainspan  (Epigenomics ag)
90
Epigenomics ag brainspan
Gene Ontology (GO) annotation was used to identify gene classes containing an overrepresentation of genes that were differentially expressed between day 0 and day 4 in iNGN cells. The majority of GO terms with an overrepresentation of downregulated genes (green) are related to cell cycle and nucleic acid metabolism, while GO terms with many upregulated genes (purple) include classes related to neuron development and physiology. For example, most genes in the Gene Ontology classification of ‘regulation of neurogenesis’ (inset) including neural progenitor markers are significantly upregulated as shown in the heatmap. RNA-Seq data of uninduced iNGN (day 0, blue) and iNGN cells (day 4, black) are compared to the Allen <t>BrainSpan</t> data, by computing the Pearson's correlation coefficients between the iNGN cells and all brain samples at each developmental time point. This shows that iNGN gene expression is more consistent with prenatal brain gene expression, and the correlation is significantly higher for day 4 iNGN cells, compared to day 0 cells (one-sided two-sample t -test, with P -values shown in red dots). Pearson's correlation coefficients were subsequently computed between day 4 iNGN cells and profiles for brain regions at each time point. The 500 most highly upregulated genes in day 4 iNGN cells were used as a neuronal signature. At each time point, Z-scores were computed for each brain region to assess their relative similarity to the iNGN signature, in comparison with the remaining brain regions. This demonstrated less similarity of iNGN cells to cortical brain structures and indicated higher similarities to the mediodorsal nucleus of thalamus, amygdaloid complex, hippocampus and cerebellar cortex. Pcw, postconception weeks.
Brainspan, supplied by Epigenomics ag, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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brainspan - by Bioz Stars, 2026-06
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brainspan: atlas of the developing human brain  (Allen Institute for Brain Science)
90
Allen Institute for Brain Science brainspan: atlas of the developing human brain
Gene Ontology (GO) annotation was used to identify gene classes containing an overrepresentation of genes that were differentially expressed between day 0 and day 4 in iNGN cells. The majority of GO terms with an overrepresentation of downregulated genes (green) are related to cell cycle and nucleic acid metabolism, while GO terms with many upregulated genes (purple) include classes related to neuron development and physiology. For example, most genes in the Gene Ontology classification of ‘regulation of neurogenesis’ (inset) including neural progenitor markers are significantly upregulated as shown in the heatmap. RNA-Seq data of uninduced iNGN (day 0, blue) and iNGN cells (day 4, black) are compared to the Allen <t>BrainSpan</t> data, by computing the Pearson's correlation coefficients between the iNGN cells and all brain samples at each developmental time point. This shows that iNGN gene expression is more consistent with prenatal brain gene expression, and the correlation is significantly higher for day 4 iNGN cells, compared to day 0 cells (one-sided two-sample t -test, with P -values shown in red dots). Pearson's correlation coefficients were subsequently computed between day 4 iNGN cells and profiles for brain regions at each time point. The 500 most highly upregulated genes in day 4 iNGN cells were used as a neuronal signature. At each time point, Z-scores were computed for each brain region to assess their relative similarity to the iNGN signature, in comparison with the remaining brain regions. This demonstrated less similarity of iNGN cells to cortical brain structures and indicated higher similarities to the mediodorsal nucleus of thalamus, amygdaloid complex, hippocampus and cerebellar cortex. Pcw, postconception weeks.
Brainspan: Atlas Of The Developing Human Brain, supplied by Allen Institute for Brain Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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brainspan: atlas of the developing human brain - by Bioz Stars, 2026-06
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Image Search Results


Gene Ontology (GO) annotation was used to identify gene classes containing an overrepresentation of genes that were differentially expressed between day 0 and day 4 in iNGN cells. The majority of GO terms with an overrepresentation of downregulated genes (green) are related to cell cycle and nucleic acid metabolism, while GO terms with many upregulated genes (purple) include classes related to neuron development and physiology. For example, most genes in the Gene Ontology classification of ‘regulation of neurogenesis’ (inset) including neural progenitor markers are significantly upregulated as shown in the heatmap. RNA-Seq data of uninduced iNGN (day 0, blue) and iNGN cells (day 4, black) are compared to the Allen BrainSpan data, by computing the Pearson's correlation coefficients between the iNGN cells and all brain samples at each developmental time point. This shows that iNGN gene expression is more consistent with prenatal brain gene expression, and the correlation is significantly higher for day 4 iNGN cells, compared to day 0 cells (one-sided two-sample t -test, with P -values shown in red dots). Pearson's correlation coefficients were subsequently computed between day 4 iNGN cells and profiles for brain regions at each time point. The 500 most highly upregulated genes in day 4 iNGN cells were used as a neuronal signature. At each time point, Z-scores were computed for each brain region to assess their relative similarity to the iNGN signature, in comparison with the remaining brain regions. This demonstrated less similarity of iNGN cells to cortical brain structures and indicated higher similarities to the mediodorsal nucleus of thalamus, amygdaloid complex, hippocampus and cerebellar cortex. Pcw, postconception weeks.

Journal: Molecular Systems Biology

Article Title: Rapid neurogenesis through transcriptional activation in human stem cells

doi: 10.15252/msb.20145508

Figure Lengend Snippet: Gene Ontology (GO) annotation was used to identify gene classes containing an overrepresentation of genes that were differentially expressed between day 0 and day 4 in iNGN cells. The majority of GO terms with an overrepresentation of downregulated genes (green) are related to cell cycle and nucleic acid metabolism, while GO terms with many upregulated genes (purple) include classes related to neuron development and physiology. For example, most genes in the Gene Ontology classification of ‘regulation of neurogenesis’ (inset) including neural progenitor markers are significantly upregulated as shown in the heatmap. RNA-Seq data of uninduced iNGN (day 0, blue) and iNGN cells (day 4, black) are compared to the Allen BrainSpan data, by computing the Pearson's correlation coefficients between the iNGN cells and all brain samples at each developmental time point. This shows that iNGN gene expression is more consistent with prenatal brain gene expression, and the correlation is significantly higher for day 4 iNGN cells, compared to day 0 cells (one-sided two-sample t -test, with P -values shown in red dots). Pearson's correlation coefficients were subsequently computed between day 4 iNGN cells and profiles for brain regions at each time point. The 500 most highly upregulated genes in day 4 iNGN cells were used as a neuronal signature. At each time point, Z-scores were computed for each brain region to assess their relative similarity to the iNGN signature, in comparison with the remaining brain regions. This demonstrated less similarity of iNGN cells to cortical brain structures and indicated higher similarities to the mediodorsal nucleus of thalamus, amygdaloid complex, hippocampus and cerebellar cortex. Pcw, postconception weeks.

Article Snippet: Given our wealth of transcriptomic information on these cells, we sought to refine this definition by comparing our RNA-Seq data with the BrainSpan Atlas dataset from the Allen Institute for Brain Science (Miller et al , ) ( http://brainspan.org/ ).

Techniques: RNA Sequencing, Gene Expression, Comparison