Table 1 A variety of search features are provided by chromoWIZ
From: chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes
Search feature | Description | Data needed |
|---|---|---|
Sequence similarity | Genes can be searched using homology either on nucleotide sequence level (BLASTN) or protein sequence level (BLASTP). | - |
Gene identifier | List of gene identifiers as provided within the genome release. | - |
Gene Ontology (GO) annotation | Genes can be searched based on their GO annotation. | - |
PFAM annotation | Genes can be searched based on their PFAM annotation. | - |
Expression variation | Gene expression levels need to vary across conditions in order to filter for interesting genes as quantified by using the coefficient of variation (sample standard deviation divided by the sample mean). | Expression matrix |
Presence of expression | The expression has to surpass a custom expression threshold in at least one condition. | Expression matrix |
Differential expression | Genes have to be in a list of genes being differentially expressed, as provided by the user. | List of differentially expressed genes |
Gene clustering | Genes have to be in a certain group of clustered genes. Clustering information is provided by the user. | Gene to cluster linkage list |