Handdrawn sketch of the neighborhood
| Many of the data types
in the previous slide are hot-linked and it is easy to generate a small web
of correlations between any transcript of interest and many other
transcripts. In this case, we have used green lines between transcripts that
have positive correlations, and red lines between transcripts that have
negative correlations. Correlations have been multiplied by 100. The
correlation of 0.96 between App and Hsp84-1 reads 96. These are Pearson product moment
correlations and they are sensitive to outliers. If you prefer, you can
recompute Spearman rank order correlations. |
|
| Where did Ndr4 (lower
left) come from? It is not in the list in the previous slide. Actually it is.
Nomenclature changes rapidly. If you click on R74996 in the previous slide
(the active webqtl version) you will see that it now has a new symbol and
name. |
|
| What are all of the conventions in this correlation
network sketch. |
|
| 1.The official gene symbol = App |
|
| 2. OUr estimate of the
location of these gene in the Mouse Genome Sequencing Consoritum version 3
build (MGSCv3). Chromosome followed by the megabase position relative to the
centromere. (Mice only have one chromosome arm so this is an unambiguous
coordinate. ) |
|
| 3. The pair of numbers:
top is the highest expression among the strain set. The lower number is the
lowest expression of that transcript among the strain set. |
|
| 4. Vertical number on
the right side of each box: this is the probe set ID given by Affymetrix. We
have truncated these probe set IDs so you will not see the usual ÒatÓ. A single gene may be
represented by more than 10 probe sets. Thus this ID number is essential to
identify the actual data source. |
|
| 5. Lower right corner: a
two digit number followed by plus and minus signs. These numbers are the
correlation value (absolute value) of the 100th best correlated transcript.
The plus and minus signs indicate the mean polarity of the correlations. |
|
| 6. The set of numbers
that read 2@140* etc. These are the approximate locations of additive effect
QTLs detected by WebQTL that we will describe in other slides. Read this as:
App has a suggestive QTL on Chr 2 at about 140 Mb and the D allele inherited
from DBA/2J confirms a higher expression level at this marker. If there is no star symbol, then it
is not even formally ÒsuggestiveÓ but does make an interesting looking blip
on the QTL radar screen. |