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Integrated annotation and analysis of in situ hybridization images using the ImAnno system: application to the ear and sensory organs of the fetal mouse.

Romand R, Ripp R, Poidevin L, Boeglin M, Geffers L, Dollé P, Poch O - PLoS ONE (2015)

Bottom Line: The results obtained from an analysis of more than 11,000 micrographs have been integrated in a newly developed knowledgebase, called ImAnno.Finally, various multilevel interaction networks were characterized, highlighting differential functional enrichments of directly or indirectly interacting genes.These analyses exemplify an under-represention of "sensory" functions in the sensory gene set suggests that E14.5 is a pivotal stage between the developmental stage and the functional phase that will be fully reached only after birth.

View Article: PubMed Central - PubMed

Affiliation: Developmental Biology and Stem Cells Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, Université de Strasbourg), BP163, 67404 Illkirch Cedex, France.

ABSTRACT
An in situ hybridization (ISH) study was performed on 2000 murine genes representing around 10% of the protein-coding genes present in the mouse genome using data generated by the EURExpress consortium. This study was carried out in 25 tissues of late gestation embryos (E14.5), with a special emphasis on the developing ear and on five distinct developing sensory organs, including the cochlea, the vestibular receptors, the sensory retina, the olfactory organ, and the vibrissae follicles. The results obtained from an analysis of more than 11,000 micrographs have been integrated in a newly developed knowledgebase, called ImAnno. In addition to managing the multilevel micrograph annotations performed by human experts, ImAnno provides public access to various integrated databases and tools. Thus, it facilitates the analysis of complex ISH gene expression patterns, as well as functional annotation and interaction of gene sets. It also provides direct links to human pathways and diseases. Hierarchical clustering of expression patterns in the 25 tissues revealed three main branches corresponding to tissues with common functions and/or embryonic origins. To illustrate the integrative power of ImAnno, we explored the expression, function and disease traits of the sensory epithelia of the five presumptive sensory organs. The study identified 623 genes (out of 2000) concomitantly expressed in the five embryonic epithelia, among which many (∼12%) were involved in human disorders. Finally, various multilevel interaction networks were characterized, highlighting differential functional enrichments of directly or indirectly interacting genes. These analyses exemplify an under-represention of "sensory" functions in the sensory gene set suggests that E14.5 is a pivotal stage between the developmental stage and the functional phase that will be fully reached only after birth.

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Dendrogram of tissue expression.The three main branches (A, B and C) are described in the main text. IE, inner ear; ME, middle ear.
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pone.0118024.g003: Dendrogram of tissue expression.The three main branches (A, B and C) are described in the main text. IE, inner ear; ME, middle ear.

Mentions: Dendrogram of tissue correlation. A distance matrix based on the expression values of the 2000 annotated genes in the 25 tissues was computed using a Spearman’s rank correlation coefficient with the following numeric values: 0: negative, 2: weak, 3: medium and 4: strong. This distance matrix was input to the FastME program [18] in order to construct a tissue expression dendrogram (Fig. 3). Clustering with the Secator program [19] is in agreement with the dendrogram. The dendrogram can be annotated and colored using the DecoreTree module directly on the web interface.


Integrated annotation and analysis of in situ hybridization images using the ImAnno system: application to the ear and sensory organs of the fetal mouse.

Romand R, Ripp R, Poidevin L, Boeglin M, Geffers L, Dollé P, Poch O - PLoS ONE (2015)

Dendrogram of tissue expression.The three main branches (A, B and C) are described in the main text. IE, inner ear; ME, middle ear.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4338146&req=5

pone.0118024.g003: Dendrogram of tissue expression.The three main branches (A, B and C) are described in the main text. IE, inner ear; ME, middle ear.
Mentions: Dendrogram of tissue correlation. A distance matrix based on the expression values of the 2000 annotated genes in the 25 tissues was computed using a Spearman’s rank correlation coefficient with the following numeric values: 0: negative, 2: weak, 3: medium and 4: strong. This distance matrix was input to the FastME program [18] in order to construct a tissue expression dendrogram (Fig. 3). Clustering with the Secator program [19] is in agreement with the dendrogram. The dendrogram can be annotated and colored using the DecoreTree module directly on the web interface.

Bottom Line: The results obtained from an analysis of more than 11,000 micrographs have been integrated in a newly developed knowledgebase, called ImAnno.Finally, various multilevel interaction networks were characterized, highlighting differential functional enrichments of directly or indirectly interacting genes.These analyses exemplify an under-represention of "sensory" functions in the sensory gene set suggests that E14.5 is a pivotal stage between the developmental stage and the functional phase that will be fully reached only after birth.

View Article: PubMed Central - PubMed

Affiliation: Developmental Biology and Stem Cells Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, Université de Strasbourg), BP163, 67404 Illkirch Cedex, France.

ABSTRACT
An in situ hybridization (ISH) study was performed on 2000 murine genes representing around 10% of the protein-coding genes present in the mouse genome using data generated by the EURExpress consortium. This study was carried out in 25 tissues of late gestation embryos (E14.5), with a special emphasis on the developing ear and on five distinct developing sensory organs, including the cochlea, the vestibular receptors, the sensory retina, the olfactory organ, and the vibrissae follicles. The results obtained from an analysis of more than 11,000 micrographs have been integrated in a newly developed knowledgebase, called ImAnno. In addition to managing the multilevel micrograph annotations performed by human experts, ImAnno provides public access to various integrated databases and tools. Thus, it facilitates the analysis of complex ISH gene expression patterns, as well as functional annotation and interaction of gene sets. It also provides direct links to human pathways and diseases. Hierarchical clustering of expression patterns in the 25 tissues revealed three main branches corresponding to tissues with common functions and/or embryonic origins. To illustrate the integrative power of ImAnno, we explored the expression, function and disease traits of the sensory epithelia of the five presumptive sensory organs. The study identified 623 genes (out of 2000) concomitantly expressed in the five embryonic epithelia, among which many (∼12%) were involved in human disorders. Finally, various multilevel interaction networks were characterized, highlighting differential functional enrichments of directly or indirectly interacting genes. These analyses exemplify an under-represention of "sensory" functions in the sensory gene set suggests that E14.5 is a pivotal stage between the developmental stage and the functional phase that will be fully reached only after birth.

Show MeSH