SigTerms: a
bioinformatics tool for linking gene expression profiling results with gene
class associations
Additional notes on searching for microRNA targeting associations
creighto@bcm.edu
Retrieving microRNA:mRNA
pairs for a set of genes and a set of microRNAs
Running the "FindSignificantTerms" macro retrieves all microRNA:mRNA pairs involving a user-specified list of
genes. In many cases, the user may have
a selected list of microRNAs of interest (e.g. from a
microRNA profiling experiment), in addition to a list
of genes. From the "Terms with
Genes" worksheet, the user can filter the retrieved microRNA:mRNA
for those that involve the list of microRNAs, by
using the Excel MATCH function with the Data Filtering feature. First, for each entry in the "Terms with
Genes" worksheet, the user looks up each microRNA
in the selected list by using the MATCH function; entries for which the microRNA was found will give a number (if "#N/A,"
the entry was not found). For novice
Excel users, screen shots of examples of using MATCH and Data Filter are
available here.
Linking mirBase
accession numbers to microRNA names (PicTar and TargetScan)
When
searching the PicTar or miRanda
target predictions, the "Terms with Genes" worksheet lists each microRNA by mirBase accession
number (e.g. "MIMAT0000072"), instead of the common microRNA name (e.g. "hsa-miR-18a"). The reason for this is that the accession
number for a particular microRNA should not change
over time, whereas the name may change from one mirBase
version to the next (e.g. a hypothetical miR-XX being
split into miR-XX-3p and miR-XX-5p).
The user
may wish to list microRNA common names alongside the mirBase accession numbers.
This is readily done using the Excel MATCH and INDEX functions, in
conjunction with the Excel table (provided here) mapping microRNA
accession numbers to common names.
First, the user looks up the row position, within the mapping table, of
each microRNA listed in the "Terms with
Genes" worksheet, using the MATCH function. Then, using the row position, the user
retrieves the common name using the INDEX function. The user can then copy the INDEX formula
values and paste them into another column, using "Paste Special"
("Paste as Values"). Screen shot examples for linking name to
accession number are available here.
Note: The "mirBase_name-to-accession.xls"
tables may list a given microRNA multiple times. The microRNA
accession-to-name mappings are listed starting with the most recent version of mirBase (v11 as of May 2008) to the oldest version (v6,
which introduced the accession numbers).
This ordering facilitates retrieving the mirBase
accession number (which should remain constant) given a common microRNA name (which may change from version to version). The MATCH and INDEX function will retrieve the
first entry starting from the top, so the most current name for a given
accession number will always be retrieved.
Note: When searching the PicTar predictions for mouse, the mirBase
accession numbers are for the human ortholog. To map from the human accession number to the
mouse accession/name, use the table provided here; you can use the MATCH
and INDEX function (screen shot examples here).
Linking microRNA families to microRNA
names (TargetScan)
When
searching the TargetScan target predictions, the
"Terms with Genes" worksheet lists each microRNA
association by family. A microRNA family may include several microRNAs
(e.g. the "let-7/98" family includes let-7a, let-7b, let-7c, let-7d,
let-7e, let-7f, let-7g, and let-7i). The
user may wish to link microRNA common names alongside
the corresponding family; however, this cannot be carried out using MATCH and
INDEX (as the mapping between family and name is not one-to-one but
one-to-many).
In order to
link microRNA family names from the "Terms with
Genes" worksheet to common names, the user can do a table join between the
worksheet named "miR_Family_info" (from the
TargetScan Annotation workbook) to the "Terms
with Genes" worksheet; this can be done using Microsoft Access. Novice Access users can do the following:
Comparing microRNA:mRNA pairs across multiple target
prediction
databases
After
searching each target prediction database separately, the user may wish to
compare the microRNA:mRNA pairs predicted from one
database with those predicted from another database. This may be done by the following: