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Figure 1
Figure 1 : This annotation web page concerns the gene Gp38. It shows the set of available ISH images (F),
information and link about the gene (A), the annotation form (B) with radio buttons to select expression value
within n.a, negative, weak, medium, strong (associated respectively to grey, blue, yellow, orange, red) and the
select boxes to choose one or several predefined keyword. The colored synthetic pictures (C,D,E) show the
expression values of each tissues.
Figure 2
Figure 2: Tissue dendrogram, based upon a hierarchical clustering using average linkage of the differentially
expressed genes. Three main branches can be distinguished:
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The branch A is related to genes from tissues mainly derived from sensory regions of the inner ear.
The branch B is more heterogeneous, although genes are mainly derived from mesenchyme tissues such
as different kinds of bones from the ribs and the otic capsule and secretary organs such as the stria
vascularis. This branch also includes the endolymphatic organ from the inner ear and the choroïde
plexus from the hindbrain as well as mesenchyme tissues from the inner ear and middle ear.
The branch C is mainly composed of genes present in nervous tissues such as the retina, and the
hindbrain and from ectodermal/mesenchymal derived tissues from the middle ear and the follicles of
vibrissae.
Figure 3
Figure 3: Examples of gene expression patterns in the sensory organs.
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A & B show the expression of Ctgf (Connective tissue growth factor) and Shc3 (Src homology 2
domain-containing transforming protein C3) in the basal cochlear canal. The cochlear canal is
delineated by dashed lines: Ko: Kölliker’s organ presents in the ventral region, Iss: inner spiral sulcus
may includes the prospective Reissner’s membrane and the outer spiral sulcus (Oss), Oc: otic capsule,
sagital section. The patchy expression of Ctgf seems to be restricted to the Kölliker’s organ extending
toward the outer spiral sulcus (Oss) and the otic capsule (Oc). Interesting enough in the Kölliker‘s organ
a region without expression (arrow) separates what could be the greater epithelial ridge from the lesser
epithelia ridge. The transcript expression of Shc3 is visible in the basal canal of the cochlea and
restricted to a small region of the Kölliker’s organ (arrows). Scale bar : 50 µm.
C & D: Expression of two genes in the utricule from the vestibular part of the inner ear. The expression
of the Cd9 (Cd 9 antigen) is visible in the prospective sensory region (Sr) of the utricule as well as the
non-sensory region (Nsr), (large arrow). The two horizontal arrows points toward the separation
between the sensory region and the non-sensory region. Mprs18c is strongly expressed in the sensory
region. Sagital sections. Scale bar: 100 µm (valid for A, B, C,D).
E & F: Two examples of transcripts expressed in the retina:Mid1 (Midline 1) and Fubp1 (Far upstream
element (FUSE) binding protein 1). Rpe: the retinal pigmented epithelium. Scale bar: 0.5 mm.
G & H: Two samples of expressed gene as observed on sagital sections of the olfactory organs. The
gene Gp38 (Glycoprotein 38 or podoplanin) is observed in the olfactory epithelium (Oe) and the
cartilage primordia of turbinate bones (Ct). The probe for Igsf4a (Immunoglobulin superfamily,
member 4A, transcript variant 2) is present all over the olfactory organ including the respiratory
epithelium (Re). Scale bar: 200 µm.
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I: Sagital sections on the primordia of vibrissae follicles. Depending of the level of the section in the
upper lip, different regions of the vibrissae present a mRNA expression. The Mif gene (Macrophage
migration inhibitory factor) is expressed in several regions of the vibrissae follicles including the
follicle cells. Expression is also observed outside the vibrissae in the surrounding mesenchyme (Me).
Scale bar: 0.5 mm.
Figure 4
Figure 4: Comparison between the distribution of gene function by using the GO database between the initial
pool of 2000 genes and those from KUROV.
A: For each GO is associated its number of genes and the percentage (versus 623 for the KUROV, in black, or
2000 for the reference set, in grey). The “NoGO” term corresponds to the set of genes for which any GO is
assigned. The “Other GOs” corresponds to the genes which didn’t appear in any of the listed GOs. The displayed
GO terms were automatically chosen by ImAnno to highlight the most significative GOs containing at least 40
genes and reducing as much as possible the overlapping categories.
B: The percentages displayed in B were calculated according to the set of 506 genes within the 623 KUROV
genes for which a GO term is assigned and for the 1634 within the 2000.
Figure 5
Figure 5-NetworkKUROV : Network analysis of 623 genes expressed in the five sensory organs (KUROV). For
this analysis we have used the STRING database along with Cytoscape. A: Out of 623 genes only 168 presented
a direct interactions (level 3) with 112 genes distributed into one principal network and 4 small ones, although
other less important networks with 4 or 5 genes were also found. The largest network is composed of 4 sub-
netwoks. B & C: Examples of what can offer mining trough the STRING database 9.05 for two genes as
illustrated by using Cytoscape: one from the sub-network 1d (Creppb) and another from the network 3
(Ndurfs3). B: Crebbp (CREB binding protein) is involved in several signaling pathways. This gene presents 9
direct connections with those of KUROV (level 3), 178 level 2 interactions with other genes (144 of them are
connected to at least two KUROV genes). C: The second example Ndufs3 is a NADH-Ubiquinone
oxidoreductase Fe-S protein 3 involved in oxidative phosphorylation. This gene is directly connected to 8 genes
from KUROV (level 3) sharing 53 genes (level 2) with Ndufb11, Ndufa9 and 1110020P15Rik.
Figure 6
Figure 6: Expression of Crebbp (a gene involved in Rubinstein-Taybi syndrome) in the five sensory organs
(KUROV).
A & B: micrographs from an ISH preparation from the basal cochlear canal including the Köllinger’s organ and
the organ of Corti (A) and the utricule from the vestibular receptors (B) as delineated by dashed lines. The
approximate sensory regions of these two organs are delimited by red ellipses. Scale bar: A: 50 µm: B: 100 µm.
C, D & E micrographs are respectively from the retina, the olfactory organ and the upper lip where several
follicules of the vibrisses present a weak mRNA expression. Scale bar: C & D : 200 µm; E: 0.5 mm.