Arntl (aka Bmal1)
Figure 1. Correlations Among Probe Sets for Arntl. This dendrogram was created using RNA
expression values estimated for 60 strains (341 individual samples). All probe sets shown target a region
that falls completely within an exonic region of Arntl defined by the brain transcriptome reconstruction
derived from RNA-Seq data on whole brain of the ILS and ISS inbred mouse strains. The distance measure
used for hierarchical clustering was one minus the Pearson correlation coefficient. Probe sets were placed
into gene clusters by ‘cutting’ the dendrogram at a height of 0.75 (thin red line). The first colored horizontal
bar at the bottom of the graphic indicates which cluster each probe set is assigned to. The second
horizontal bar indicates the portion of samples with expression values detected above background (DABG)
with colors ranges from white (50% of samples) to black (100% of samples). The cluster that is highlighted
in the yellow box with a red border was identified as a candidate gene for a predisposition to variation in
alcohol consumption in the drinking in the dark paradigm.
Figure 2 . Transcript Structure of Arntl and Relevant Exon Array Probe Sets. In the top track in the
UCSC Genome Browser (http://genome.ucsc.edu), Brain Transcriptome Reconstruction, are the high
confidence transcripts identified in the brain transcriptome reconstruction of the ILS and ISS inbred mouse
strains. The second track, Arntl – exon array probesets (3 clusters), contains the probe sets from the
Affymetrix Mouse Exon 1.0 ST Array that fall completely within an exonic region of the single splice variant
of Arntl derived from the brain transcriptome reconstruction (labeled total.58355.1 in the top track). Probe
sets are colored based on what cluster they were assigned to according to their correlation structure and
match the colors shown in Figure 1. The probe sets in green are part of the gene cluster identified as a
candidate gene for a predisposition to variation in alcohol consumption in the drinking in the dark paradigm.
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Gtf3c1
Figure 3. Correlations Among Probe Sets for Gtf3c1. This dendrogram was created using RNA
expression values estimated for 60 strains (341 individual samples). All probe sets shown target a region
that falls completely within an exonic region of Gtf3c1 defined by the brain transcriptome reconstruction
derived from RNA-Seq data on whole brain of the ILS and ISS inbred mouse strains. The distance measure
used for hierarchical clustering was one minus the Pearson correlation coefficient. Probe sets were placed
into gene clusters by ‘cutting’ the dendrogram at a height of 0.75 (thin red line). The first colored horizontal
bar at the bottom of the graphic indicates which cluster each probe set is assigned to. The second
horizontal bar indicates the portion of samples with expression values detected above background (DABG)
with colors ranges from white (50% of samples) to black (100% of samples). The cluster that is highlighted
in the yellow box with a red border was identified as a candidate gene for a predisposition to variation in
alcohol consumption in the drinking in the dark paradigm.
Figure 4. Transcript Structure of Gtf3c1 and Relevant Exon Array Probe Sets. In the top track in the
UCSC Genome Browser (http://genome.ucsc.edu), Brain Transcriptome Reconstruction, are the high
confidence transcripts identified in the brain transcriptome reconstruction of the ILS and ISS inbred mouse
strains. The second track, Gtf3c1 – exon array probesets (7 clusters), contains the probe sets from the
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Affymetrix Mouse Exon 1.0 ST Array that fall completely within an exonic region of either of the two splice
variants of Gtf3c1 derived from the brain transcriptome reconstruction (labeled total.3906.1 and total.3906.2
in the top track). Probe sets are colored based on what cluster they were assigned to according to their
correlation structure and match the colors shown in Figure 3. The probe set in blue is the gene cluster
identified as a candidate gene for a predisposition to variation in alcohol consumption in the drinking in the
dark paradigm.
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Pld5
Figure 5. Correlations Among Probe Sets for Pld5. This dendrogram was created using RNA expression
values estimated for 60 strains (341 individual samples). All probe sets shown target a region that falls
completely within an exonic region of Pld5 defined by the brain transcriptome reconstruction derived from
RNA-Seq data on whole brain of the ILS and ISS inbred mouse strains. The distance measure used for
hierarchical clustering was one minus the Pearson correlation coefficient. Probe sets were placed into gene
clusters by ‘cutting’ the dendrogram at a height of 0.75 (thin red line). The first colored horizontal bar at the
bottom of the graphic indicates which cluster each probe set is assigned to. The second horizontal bar
indicates the portion of samples with expression values detected above background (DABG) with colors
ranges from white (50% of samples) to black (100% of samples). The cluster that is highlighted in the yellow
box with a red border was identified as a candidate gene for a predisposition to variation in alcohol
consumption in the drinking in the dark paradigm.
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Figure 6. Transcript Structure of Pld5 and Relevant Exon Array Probe Sets. In the top track in the
UCSC Genome Browser (http://genome.ucsc.edu), Brain Transcriptome Reconstruction, are the high
confidence transcripts identified in the brain transcriptome reconstruction of the ILS and ISS inbred mouse
strains. The second track, Pld5 – exon array probesets (2 clusters), contains the probe sets from the
Affymetrix Mouse Exon 1.0 ST Array that fall completely within an exonic region of any of the four splice
variants of Pld5 derived from the brain transcriptome reconstruction (labeled total.3545.1, total.3545.2,
total.3545.3 and total.3545.4 in the top track). Probe sets are colored based on what cluster they were
assigned to according to their correlation structure and match the colors shown in Figure 5. The probe sets
in blue are included in the gene cluster identified as a candidate gene for a predisposition to variation in
alcohol consumption in the drinking in the dark paradigm.
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Trim62
Figure 7. Correlations Among Probe Sets for Trim62. This dendrogram was created using RNA
expression values estimated for 60 strains (341 individual samples). All probe sets shown target a region
that falls completely within an exonic region of Trim62 defined by the brain transcriptome reconstruction
derived from RNA-Seq data on whole brain of the ILS and ISS inbred mouse strains. The distance measure
used for hierarchical clustering was one minus the Pearson correlation coefficient. Probe sets were placed
into gene clusters by ‘cutting’ the dendrogram at a height of 0.75. The first colored horizontal bar at the
bottom of the graphic indicates which cluster each probe set is assigned to. The second horizontal bar
indicates the portion of samples with expression values detected above background (DABG) with colors
ranges from white (50% of samples) to black (100% of samples). For this gene all probe sets were
correlated and placed into a single cluster. This cluster, highlighted in the yellow box with a red border, was
identified as a candidate gene for a predisposition to variation in alcohol consumption in the drinking in the
dark paradigm.
Figure 8. Transcript Structure of Trim62 and Relevant Exon Array Probe Sets. In the top track in the
UCSC Genome Browser (http://genome.ucsc.edu), Brain Transcriptome Reconstruction, are the high
confidence transcripts identified in the brain transcriptome reconstruction of the ILS and ISS inbred mouse
strains. The second track, trim62 – exon array probesets (1 cluster), contains the probe sets from the
Affymetrix Mouse Exon 1.0 ST Array that fall completely within an exonic region of any of the single splice
variant of Pld5 derived from the brain transcriptome reconstruction (labeled total.62629.1 in the top track).
Probe sets are colored based on what cluster they were assigned to according to their correlation structure
and match the colors shown in Figure 7. The probe sets in green are included in the gene cluster identified
as a candidate gene for a predisposition to variation in alcohol consumption in the drinking in the dark
paradigm.
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Wrn
Figure 9. Correlations Among Probe Sets for Wrn. This dendrogram was created using RNA expression
values estimated for 60 strains (341 individual samples). All probe sets shown target a region that falls
completely within an exonic region of Wrn defined by the brain transcriptome reconstruction derived from
RNA-Seq data on whole brain of the ILS and ISS inbred mouse strains. The distance measure used for
hierarchical clustering was one minus the Pearson correlation coefficient. Probe sets were placed into gene
clusters by ‘cutting’ the dendrogram at a height of 0.75 (thin red line). The first colored horizontal bar at the
bottom of the graphic indicates which cluster each probe set is assigned to. The second horizontal bar
indicates the portion of samples with expression values detected above background (DABG) with colors
ranges from white (50% of samples) to black (100% of samples). The cluster that is highlighted in the yellow
box with a red border was identified as a candidate gene for a predisposition to variation in alcohol
consumption in the drinking in the dark paradigm.
Figure 10. Transcript Structure of Wrn and Relevant Exon Array Probe Sets. In the top track in the
UCSC Genome Browser (http://genome.ucsc.edu), Brain Transcriptome Reconstruction, are the high
confidence transcripts identified in the brain transcriptome reconstruction of the ILS and ISS inbred mouse
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strains. The second track, Wrn – exon array probesets (11 clusters), contains the probe sets from the
Affymetrix Mouse Exon 1.0 ST Array that fall completely within an exonic region of either of the two splice
variants of Wrn derived from the brain transcriptome reconstruction (labeled total.1614.1 and total.1614.2 in
the top track). Probe sets are colored based on what cluster they were assigned to according to their
correlation structure and match the colors shown in Figure 9. The probe set in purple is the gene cluster
identified as a candidate gene for a predisposition to variation in alcohol consumption in the drinking in the
dark paradigm.
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