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Create Gene Lists with Gene Filters
Select a Gene Filter Type
Creating or importing Gene Lists is the first step in most gene-centric analysis for
microarray experiments. Saved Gene Lists can be managed and used in advanced microarray data
analysis methods.
1. Expression Profile-Based Filters
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This is the most important type of gene filters. They are mainly used to identify
differentially-expressed genes (probe sets).
A. Single Experiment Expression Profile
Filter -- Run one or several filters on one experiment. The filter can
also be a composite filter from several filters
through
Boolean operstors. Filters are based on statistical test, absolute value range, relative and
absolute variation, fold of change, MAS5.0 Present/Absent call or other
variation measures.
B. Cross-Experiment Expression Profile
Filter -- Run a filter on one or several experiments in parallel.
The probe sets meeting criteria in all selected experiments will be saved to
gene list. Different experiments may be combined to a "single" psudo-experiment
for fold change filter.
C.
Co-Expressed Genes
Filter -- Find probe sets showing similar expression profiles to
seed probe set.
2. Function2Expression -- Biological Filters from Gene
Functional Annotation to Expression Profile
This is a collection of gene list creation methods, based on several types of
gene functional annotations.
A. GO2Expression -- Browse and search Gene Ontology
tree, and retrieve probe sets or
genes from selected GO classes.
B. Pathway2Expression
-- Find probe
sets corresponding to enzymes from your interested metabolic or regulatory
pathways. Available for the Arabidopsis ATH1 GeneChip only. Based on KEGG and
TAIR pathway data.
C. Domain2Expression -- Creates Gene lists
corresponding to predicted InterPro protein functional domains. Most of the functional domain information
comes from UniProt, TIGR. For other non-characterized exemplars, BarleyBase
conducts in-house annotation on with InterproScan.
D. GeneFamily2Expression -- Find probe
sets corresponding to a given gene family. Available for the Arabidopsis ATH1
GeneChip only.
E.
Keyword2Expression -- Find probe sets matching single or several terms
in exemplar annotation.
F. Map2Expression -- Finding genes by their
genetic map locations, in order to associate gene expression with known
QTLs --Demo for Barley only.
G.
BLAST2Expression--
Finding
probe sets whose exemplars have similarity to your own sequences.
Cross-Platform is another form of
BLAST2Expression.
3. Retrieve Users Own Gene Lists
A. Import Gene List Filter -- You may input
a list of probe sets or exemplar names and retrieve their expression from
selected experiment. You can input any free text containing the
probe set names.
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