BarleyBase Query Help I: Experiment Search
Contents
The
Experiment Query is designed to allow the user to search and browse
the experiments, protocols and array designs. Experiment query can choose
various criteria to select experiments. The criteria include Experiment
Type, Experimental Factors, Species, Submitter's name and Institution,
Affymetrix GeneChip Array, and, Protocol.
Usage
1. Select "Experiment
Query" item from the menu under "Database Usage".
2. Select values for your interested criteria from the corresponding
drop-down list.
3. Press "Query" button to conduct the query.
4. On the resulting page, choose the experiment you are interested in,
and press the small green icon to the right of title to go to detailed
view.
5. In the details page, use "Show Details" to show more detail on
provider and hybridizations, use "Hide Details" to hide details.
BarleyBase Query Help II: Microarray Elements/Probe Sets Search
Contents
The probe set query is designed to allow the user to find a subset of
microarray elements based on expression, annotation and sequence
information for data retrieval and analysis.
According to the criteria used, the probe set query can be classified
to 5 groups.
1. Search by Gene
Expression Profiles: User can select one
experiment, and find probe sets showing desired expression profile in
absolute value and variation using multiple filters.
2. Probe Set Name-Based Search: Select one
Probe Set Name to align it with exemplar sequence, or search for a
list of
Probe Set Names.
3. Keyword-Based Search: User can
construct complex search term with keywords and Boolean operators to
search against the exemplar sequence annotation information. For
Barley1 GeneChip, this will be the information from the top BLAST hits
sequences from other species. Due to the nature of annotation, this query
will only find a VERY LIMITED subset of probe
sets in Barley1 GeneChip. Arabidopsis sequences are well-annotated, so the
keyword-based query will be very exhaustive..
4. Query by
Pathway or
Gene
Family Membership: These queries working for Arabidopsis
only. The queries starts from lists of
KEGG Arabidopsis pathways, or
the TAIR-compiled gene families.
There are 5,246 genes assigned to 736 gene families in Arabidopsis. For
ATH1-121501 GeneChip,4,014 probe sets are assigned to the gene families.
Currently, 2000+ ATH1-121501 GeneChip probe sets can be assigned to
KEGG pathways.
5. Sequence Similarity-Based Search at
BarleyBase BLAST: Search for Barley1 and Arabidopsis
ATH1-121501 GeneChip Exemplar Sequences.
Usage
General Steps in Probe Set Query:
1. Select the query type from the menu under "Database Usage" -->
"Probe Set Query".
2. Select values for your interested criteria following instructions on
the query setup pages.
3. Press the appropriate buttons according to aims to conduct the
query.
4. On the resulting page, qualify probe sets are presented in HTML
table format, either as annotation view, or as expression view according
to instruction.
5. Go to details for specific probe sets following hyperlinks.
6. Analyze retrieved dataset within BarleyBase if applicable.
Specific Steps in a Given Probe Set Query Type:
1. Select "Query
by Expression Profile" item from the menu under "Database Usage" -->
"Probe Set Query".
2. Select the experiment and expression estimation/normalization method
from drop-down lists
3. Click "Summary" to view details for each
hybridizations of the experiment for aiding in choosing parameters.
4. Select one or more filters by checking the checkbox on the left of
the
filters. The "Multiple filter" or "Composite Filter" button must be checked if you want to run several filters in a
time, otherwise, only the first checked filter will be used.
5. In "Advanced Filter"
page, customize a combined filter in textbox of filter 9 with Boolean
operators. If not specified, each checked filter will be run separately.
If specified, the combined filter will be run along with the separate
filters.
6. Press "Run" button to conduct the query.
7. On the resulting page, choose ONE filter result you are interested
in by checking the checkbox. Note: If more than one is checked, only the
first checked one will be used.
8. View details of the filtered probe sets in HTML table format by pressing the
"View Annotation" or "View Expression" buttons.
9. Alternatively, download the results in tab-delimited formats by
pressing the "Download/Analyze".
10. To analyze the data set, follow step 9, at the result page, click
"Download/Analyze" to do hierachical clustering, K-Means partition,
SOM, Sammon's multidimensional scaling (MDS) or principla Component
Analysis (PCA).
1. Select "Query
by Probe Set Name" item from the menu under "Database Usage" -->
"Probe Set Query".
2. Select the experiment that you are interested. from drop-down lists
3. Enter the list of probe set names into the textarea. Please separate
names with comma. For example, "AF032687_at , AF039024_at , AF052395_at ,
AF052396_at , U19359_s_at , U29604.1_at".
4. Press "Query" button to conduct the query.
5. On the resulting page, get details of a given probe set following
hyperlinks.
User can construct complex search term with keywords and Boolean
operators to
search against the exemplar sequence annotation information
1. Select "Query
by Keyword" item from the menu under "Database Usage" --> "Probe Set
Query".
2. Select the GeneChip type, result display type with radio boxes.
3. Select the experiment and expression estimation/normalization method
from drop-down lists
4. Construct search term in textbox. (1). Enclose keywords (case
insensitive) in double quotes, (2). separated them by "AND" or "OR" (in
uppercase), (3). define precedence with parentheses. Example: "disease"
AND ("protein kinase" OR "membrane protein").
6. Press "Search" button to conduct the query.
7. On the resulting page, get details of a given probe set following
hyperlinks.
1. Select "Query
by Gene Family" or "Query
by Pathway" item from the menu under
"Database Usage" --> "Probe Set Query".
2a. For query by gene-family, first select the experiment and
expression estimation/normalization method from drop-down lists, then
click the "Genes" link to view the annotation, click the "Expression" link
to view expression values.
2b. For query by pathway, click on a KEGG pathway name.
3. Select the experiment and expression estimation/normalization method
from drop-down lists
4. To view sequences for a given enzyme in the pathway, click on the
green rectangle, all probe sets corresponding to the enzyme will be
retrieved. Only enzymes colored in green may have probe sets associated
with it (from 0 to several entries).
5.To retrieved all probe sets related to current pathway, use the "Get
All Annotation" button for annotation, use the "Get All Expression" button
for expression values.
6. On the resulting pages, get details of a given probe set following
hyperlinks.
-
Sequence Similarity-Based Search at
BarleyBase BLAST
1. Select "BarleyBase
BLAST" item from the menu under "Tools".
2. Paste in the text area your won sequence in FASTA format.
3. Choose "Barley1" or "Arabidopsis" exemplar sequence as data from
"Database" field.
4. Select appropriate BLAST type from drop-down list.
5. Optionally set up other advanced options. You may consult the links
to NCBI's help for the options.
6.Press "Blast" button to conduct the search.
To retrieved all probe sets related to current pathway, use the "Get
All Annotation" button for annotation, use the "Get All Expression" button
for expression values.
7. On the resulting pages, get details of a top hit Barley1 exemplars.
The interactive browsing of results, and the menu bars requires
JavaScript be turned on in your browser.
-
Do not use popup-ad blocking function in browser setting or
with third-party utilities, because JavaScript-enabled popup windows are
used extensively in BarleyBase.
-
For MS Internet Explorer:
-
On the Tools menu, select Internet Option.
-
Click Security-->Click "Internet" icon --> Custom Level.
-
Under Scriptiing, select "Enable"
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