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A gene expression resource generated by genome-wide lacZ profiling in the mouse.

Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA, Souter L, Siragher E, Lillistone C, Green AL, Wardle-Jones H, Carragher DM, Karp NA, Smedley D, Adams NC, Sanger Institute Mouse Genetics ProjectBussell JN, Adams DJ, Ramírez-Solis R, Steel KP, Galli A, White JK - Dis Model Mech (2015)

Bottom Line: Strong agreement was observed, indicating a high degree of specificity in our data.Furthermore, there were 1207 observations of expression of a particular gene in an anatomical structure where Bgee had no data, indicating a large amount of novelty in our data set.Examples of expression data corroborating and extending genotype-phenotype associations and supporting disease gene candidacy are presented to demonstrate the potential of this powerful resource.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.

No MeSH data available.


Related in: MedlinePlus

The granularity of annotation was extended in the brain. (A) The percentage of genes for which lacZ reporter gene expression was detected in the brain, spinal cord, peripheral nervous system and seven selected brain sub-structures. The percentage was calculated based on the subset of 125 genes for which the extended brain annotation was performed (Table S1). (B-G) Examples of expression patterns in the brain included the following: (B) ubiquitous expression of Slc25a28; (C,E) olfactory lobe, cerebral cortex, hippocampus, striatum, hypothalamus, cerebellum and brainstem expression of Dpm1 (C) and Ankrd6 (E); (D) olfactory lobe, cerebral cortex, hippocampus, hypothalamus, cerebellum and brainstem expression of Medag; (F) cerebral cortex, hippocampus and brainstem expression of 3110035E14Rik; and (G) olfactory lobe, cerebral cortex and striatum expression of Kcnh4. Olfactory lobe (OL), cerebral cortex (CC), hippocampus (HPC), striatum (STR), hypothalamus (HY), cerebellum (CB) and brainstem (BS). Scale bar: 2 mm.
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DMM021238F3: The granularity of annotation was extended in the brain. (A) The percentage of genes for which lacZ reporter gene expression was detected in the brain, spinal cord, peripheral nervous system and seven selected brain sub-structures. The percentage was calculated based on the subset of 125 genes for which the extended brain annotation was performed (Table S1). (B-G) Examples of expression patterns in the brain included the following: (B) ubiquitous expression of Slc25a28; (C,E) olfactory lobe, cerebral cortex, hippocampus, striatum, hypothalamus, cerebellum and brainstem expression of Dpm1 (C) and Ankrd6 (E); (D) olfactory lobe, cerebral cortex, hippocampus, hypothalamus, cerebellum and brainstem expression of Medag; (F) cerebral cortex, hippocampus and brainstem expression of 3110035E14Rik; and (G) olfactory lobe, cerebral cortex and striatum expression of Kcnh4. Olfactory lobe (OL), cerebral cortex (CC), hippocampus (HPC), striatum (STR), hypothalamus (HY), cerebellum (CB) and brainstem (BS). Scale bar: 2 mm.

Mentions: The endogenous expression pattern of each gene was assessed in up to 47 tissues.lacZ reporter gene whole-mount analysis was performed to ascertain the expression profile of each gene of interest. Examples are presented of expression in each of the entities annotated. The genotype is stated for each panel. (A) Testis (T); epididymis was excluded because of endogenous background staining. (B) Male urogenital system with prostate (black arrowhead) and urinary tract staining on the urinary bladder (UB). (A,B) Vas deferens (red arrowhead). (C) Female reproductive system with the ovary (O), oviduct (OV) and uterus (U). (D) Mammary gland. (E) Brain (inner cerebral cortex; see Fig. 3 for expression in other annotated brain sub-structures). (F) Spinal cord grey matter. (G) Cranial cavity including the pituitary (black arrowhead) and peripheral nerve (trigeminal ganglia) staining (white arrowheads). (H) Trachea, thyroid (TH) and parathyroid glands (arrows). (I) Lung. (J) Kidney. (K) Cartilaginous rib (black arrows). (K,L) Skeletal muscle (asterisks). (L) Hindlimb with bone staining (B) on the tibia. (L,M) Vascular staining on blood vessels (red arrow). (N) Heart and aorta (arrow). (O) Adrenal medulla. (P) Pancreas. (Q) Skin. (R) Stomach and oesophagus (arrowhead). (S) Small intestine and Peyer's patches (arrowhead). (T) Large intestine. (U) Colon. (V) Liver and gall bladder (arrow). (W) Mesenteric lymph nodes. (X) Thymus. (Y) Spleen. (Z) Eye. (AA) Brown adipose tissue. (AB) White adipose tissue.


A gene expression resource generated by genome-wide lacZ profiling in the mouse.

Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA, Souter L, Siragher E, Lillistone C, Green AL, Wardle-Jones H, Carragher DM, Karp NA, Smedley D, Adams NC, Sanger Institute Mouse Genetics ProjectBussell JN, Adams DJ, Ramírez-Solis R, Steel KP, Galli A, White JK - Dis Model Mech (2015)

The granularity of annotation was extended in the brain. (A) The percentage of genes for which lacZ reporter gene expression was detected in the brain, spinal cord, peripheral nervous system and seven selected brain sub-structures. The percentage was calculated based on the subset of 125 genes for which the extended brain annotation was performed (Table S1). (B-G) Examples of expression patterns in the brain included the following: (B) ubiquitous expression of Slc25a28; (C,E) olfactory lobe, cerebral cortex, hippocampus, striatum, hypothalamus, cerebellum and brainstem expression of Dpm1 (C) and Ankrd6 (E); (D) olfactory lobe, cerebral cortex, hippocampus, hypothalamus, cerebellum and brainstem expression of Medag; (F) cerebral cortex, hippocampus and brainstem expression of 3110035E14Rik; and (G) olfactory lobe, cerebral cortex and striatum expression of Kcnh4. Olfactory lobe (OL), cerebral cortex (CC), hippocampus (HPC), striatum (STR), hypothalamus (HY), cerebellum (CB) and brainstem (BS). Scale bar: 2 mm.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4631787&req=5

DMM021238F3: The granularity of annotation was extended in the brain. (A) The percentage of genes for which lacZ reporter gene expression was detected in the brain, spinal cord, peripheral nervous system and seven selected brain sub-structures. The percentage was calculated based on the subset of 125 genes for which the extended brain annotation was performed (Table S1). (B-G) Examples of expression patterns in the brain included the following: (B) ubiquitous expression of Slc25a28; (C,E) olfactory lobe, cerebral cortex, hippocampus, striatum, hypothalamus, cerebellum and brainstem expression of Dpm1 (C) and Ankrd6 (E); (D) olfactory lobe, cerebral cortex, hippocampus, hypothalamus, cerebellum and brainstem expression of Medag; (F) cerebral cortex, hippocampus and brainstem expression of 3110035E14Rik; and (G) olfactory lobe, cerebral cortex and striatum expression of Kcnh4. Olfactory lobe (OL), cerebral cortex (CC), hippocampus (HPC), striatum (STR), hypothalamus (HY), cerebellum (CB) and brainstem (BS). Scale bar: 2 mm.
Mentions: The endogenous expression pattern of each gene was assessed in up to 47 tissues.lacZ reporter gene whole-mount analysis was performed to ascertain the expression profile of each gene of interest. Examples are presented of expression in each of the entities annotated. The genotype is stated for each panel. (A) Testis (T); epididymis was excluded because of endogenous background staining. (B) Male urogenital system with prostate (black arrowhead) and urinary tract staining on the urinary bladder (UB). (A,B) Vas deferens (red arrowhead). (C) Female reproductive system with the ovary (O), oviduct (OV) and uterus (U). (D) Mammary gland. (E) Brain (inner cerebral cortex; see Fig. 3 for expression in other annotated brain sub-structures). (F) Spinal cord grey matter. (G) Cranial cavity including the pituitary (black arrowhead) and peripheral nerve (trigeminal ganglia) staining (white arrowheads). (H) Trachea, thyroid (TH) and parathyroid glands (arrows). (I) Lung. (J) Kidney. (K) Cartilaginous rib (black arrows). (K,L) Skeletal muscle (asterisks). (L) Hindlimb with bone staining (B) on the tibia. (L,M) Vascular staining on blood vessels (red arrow). (N) Heart and aorta (arrow). (O) Adrenal medulla. (P) Pancreas. (Q) Skin. (R) Stomach and oesophagus (arrowhead). (S) Small intestine and Peyer's patches (arrowhead). (T) Large intestine. (U) Colon. (V) Liver and gall bladder (arrow). (W) Mesenteric lymph nodes. (X) Thymus. (Y) Spleen. (Z) Eye. (AA) Brown adipose tissue. (AB) White adipose tissue.

Bottom Line: Strong agreement was observed, indicating a high degree of specificity in our data.Furthermore, there were 1207 observations of expression of a particular gene in an anatomical structure where Bgee had no data, indicating a large amount of novelty in our data set.Examples of expression data corroborating and extending genotype-phenotype associations and supporting disease gene candidacy are presented to demonstrate the potential of this powerful resource.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.

No MeSH data available.


Related in: MedlinePlus