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Gene Search

Gene searches will take you to a gene information page that may contain the following information, depending on the gene:

  • Arabidopsis Ortholog
    • Arabidopsis Gene Accession
    • Evalue - From BLAST of Camelina peptide to Arabidopsis peptide
    • Ath Description - Description line from fasta file
    • GO Terms - Arabidopsis GO Molecular Function terms from Tair
    • GO Slim Terms - Arabidopsis GO Slim Molecular Function terms from Tair
    • Aralip Pathways - Pathway annotation from the Aralip database
    • Lipid Gene DB Groups - Lipid gene annotation from the Indiana Univesity Lipid Gene Database
  • Camelina Information
    • Syntenic sub-genome and Homeologs - Synteny calls from Kagale, et al.
    • TF Family - Transcription factor family assignment
    • Gene Expression - Expression data across all public experiments included in this database
  • Co-expression Table - The top (+/-) 50 Pearson corelation coefficients (PCC)

Results

Gene information pages contain information about the assigned Arabidopsis ortholog, as well as gene expression and co-expression data computed in-house from publically avaialable RNAseq reads.

Publically available annotation about the samples used can be found on the Biosamples page. This information is integrated into the gene expression results that are linked from gene information pages. Gene expression results can be obtained directly by entering the gene accession on the Gene Expression search page. Heatmaps displaying a set of experssion data for Camelina genes can be obtained on the Heatmap page.

Regulation

Search by Transcription factor family to find Camelina genes within that family. Make search parameters more precise by adding a Camelina gene accession number to the search (not required).

Results

Transcription factor family page contains information about genes within a specific transcription factor family. Results will then display the same as a “gene search” query.

Gene Expression Search

Search by gene accession number to see expression information.
Drop down menu gives functionality to see a heat map of gene expression results with various options and examples are provided on tab.

Syntelogs

Determine relationships between Camelina and Arabidopsis genes by searching for a gene. Enter a partial gene name to display a series of genes that fit your query.Results can be downloaded in CSV format