Mouse-Chicken Transcriptome Comparisons: Home

Search: Enter a single mouse or chicken Ensembl gene ID or a mouse gene symbol used by Ensembl release 61.

Get correlated genes: Enter a single mouse or chicken Ensembl gene ID or a mouse gene symbol used by Ensembl release 61.

Quick sort: Genes sorted by specificity in mouse regions (in comparison to other mouse regions; mouse gene symbols having one to one orthologs in chicken): Dorsal cortex, Layer A, Dorsal cortex, Layer B, Dorsal cortex, Layer C, Dorsal cortex, Layer D, Dorsal cortex, Layer E, Dorsal cortex, Layer F, Lateral cortex, Layer A, Lateral cortex, Layer B, Lateral cortex, Layer C, Lateral cortex, Layer D, Lateral cortex, Layer E, Lateral cortex, Layer F, Claustrum-Endopiriform, Hippocampus, Pallial amygdala, Striatum
Genes sorted by specificity in chicken regions (in comparison to other chicken regions; mouse gene symbols of one to one orthologs): Arcopallium, Mesopallium, Nidopallium, Hyperpallium, Dorsolateral cortex, Hippocampus, Striatum

Advanced sort: Sort genes by conformity to a requested pattern of relative expression. The specificity index is bounded between -1 (perfect mismatch) and 1 (perfect match) and is calculated as the sum of the specificities in the merged regions (minus the specificities of 'low' regions). When the search includes regions from both species the reported specificity index is the unweighted average for the two species.
Dorsal cortex A
(Layers 2/3)
Low
Don't care
High
Dorsal cortex B
(Upper Layer 4)
Low
Don't care
High
Dorsal cortex C
(Lower Layer 4, Layer 5)
Low
Don't care
High
Dorsal cortex D
(Layer 5)
Low
Don't care
High
Dorsal cortex E
(Layer 6)
Low
Don't care
High
Dorsal cortex F
(Layers 6 & 6b)
Low
Don't care
High
Lateral cortex A
(Layers 2/3)
Low
Don't care
High
Lateral cortex B
(Layer 4)
Low
Don't care
High
Lateral cortex C
(Lower Layer 4, Layer 5)
Low
Don't care
High
Lateral cortex D
(Layers 5 & 6)
Low
Don't care
High
Lateral cortex E
(Layer 6)
Low
Don't care
High
Lateral cortex F
(Layers 6 and 6b)
Low
Don't care
High
Claustrum-endopiriform
(Mouse)
Low
Don't care
High
Hippocampus
(Mouse)
Low
Don't care
High
Pallial amygdala
(Mouse)
Low
Don't care
High
Striatum
(Mouse)
Low
Don't care
High
Arcopallium
(Chicken)
Low
Don't care
High
Mesopallium
(Chicken)
Low
Don't care
High
Nidopallium
(Chicken)
Low
Don't care
High
Hyperpallium
(Chicken)
Low
Don't care
High
Dorsolateral cortex
(Chicken)
Low
Don't care
High
Hippocampus
(Chicken)
Low
Don't care
High
Striatum
(Chicken)
Low
Don't care
High

Find functional annotations associated with a gene: Enter a single mouse gene symbol or gene ID used by Ensembl.

Browse functional annotations

Search functional annotations: Enter keywords to search functional annotations. Search is case insensitive but word order matters.

Correspondence of the dissected samples to layers (red reflects higher expression):

The heatmaps were made with Matrix2png. Values reflect the calculation described in Figure 2 of the Neuron paper, though using only genes that were annotated to be specific markers of each layer.

Only the top 5000 most highly expressed (in at least one species) one-to-one orthologs between chicken and mouse are included in this analysis.

Please direct questions about the website to Grant Belgard. This site is not intended for programatic access.

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