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3. PhenoBlast

PhenoBlast Search the most similar alleles within this database to the query allele user specified.

3.1. Starting PhenoBlast with default settings

i). The easy way to use PhenoBlast is that user can input a query allele in the input box of Step 1 and then press the " Run PhenoBlast" button with default settings.

ii). When user input any characters or a partial word in the input box, system will automatically generate a pull-down menu, listing all allele names containing keyword user specified similar to Google Suggestion. User can simply choose a allele to be a query allele.


3.2. Starting PhenoBlast with customized settings

i). All parameters are grouped into 5 steps according to parameter type.

ii). In " Step 1", three parameters are within this step, including query allele input box, how many rows will show in the result pages and order-by information. order-by information means how PhenoBlast order the result. Currently the system provide four choices, such as
  1. " All Matched Features"
    It means that features show significant or non significant changes compare to corresponding ones of wild-type in both query allele and a hit allele in this database simultaneously.
  2. " All Deviant Features"
    It means that features show significant changes compare to corresponding ones of wild-type in both query allele and a hit allele in this database simultaneously. It contains " Increased Deviant Features"," Decreased Deviant Features"
  3. " Increased Deviant Features"
    It means that features show significantly increased deviances compare to corresponding ones of wild-type in both query allele and a hit allele in this database simultaneously. Detailed information please link to Phenotype Feature.
  4. " Decreased Deviant Features"
    It means that features show significantly decreased deviances compare to corresponding ones of wild-type in both query allele and a hit allele in this database simultaneously. Detailed information please link to Phenotype Feature.

iii). In " Step 2", Mutation Deviation features are selected in this step.
Detailed information about features please link to Phenotype Feature.

iv). In " Step 3", Temperature Deviation features are selected in this step.
Detailed information about features please link to Phenotype Feature.

iv). In " Step 4", Cell Cycle Deviation features are selected in this step.
Cell Cycle Flux features mean :
  1. the comparison between features in Unbud and corresponding ones in Small Bud at the same temperature ( 26 C or 32 C).
  2. the comparison between features in Small Bud and corresponding ones in Medium Bud at the same temperature ( 26 C or 32 C).
  3. the comparison between features in Medium Bud and corresponding ones in Large Bud at the same temperature ( 26 C or 32 C).
Detailed information about features please link to Phenotype Feature.

v). In " Step 5", Ontology and Set Cutoff is selected in this step.
This database integrated a function of go enrichment analysis implemented by GO-TermFinder.
The genes of top fifty hit alleles in PhenoBlast result are used to execute go enrichment analysis.


PhenoBlast Result Example Interface

Go Term Finder Result Interface

PhenoBlast Result Align

Powered By Boone, Andrews and Zhang Labs
Last database updated September 8, 2011 PhenoM 1.0