Gene coexpression data in ALCOdb

Coexpression data provided in ALCOdb.

Details of the data can be found on the download page in ALCOdb. http://alcodb.jp/coexpression/download

• Coexpression data
  • Cre.v15-08.G15519-S172.quantile.mrgeo.d.zip
  • Cre.v15-02.G15540-S180.qnorm.mrgeo.d.zip
  • Cre.v13-10.G18773-S137.qnorm.mrgeo.d.zip
  • Cme1.v14-06.G4586-S75.d.zip
  • Cme2.v14-06.G6506-S48.d.zip
• Gene expression table to calculate the coexpression data
  • Cre-R1-15-08_GeneExpressionTable.tsv.gz
  • Cme1_GeneExpressionTable.tsv.zip
  • Cme2_GeneExpressionTable.tsv.zip  
• Codon usage similarity for evaluation
  • Cre_v55.CodonUsage.G17741.zip

Data Format

Gene coexpression data folder contains a number of files, and file names correspond to the query gene IDs. Each file includes the coexpressed gene list as in the following format (Example about Cre01g001400 in cre.v15-08.G15519-S172.quantile.mrgeo.d).

• File Name: Cre01g001400
• Line1: Cre03g197300    1.00    0.8352
• Line2: Cre13g605200    6.63    0.6938
• Line3: Cre09g411751    7.35    0.7082
• Line4: Cre15g638551    9.38    0.7128
• Line5: Cre01g037600    10.25    0.6761

• Columns are tab-deliminated.
• Lines are sorted by column2.
• Column1: ID of coexpressed gene.
• Column2: Matual Rank (MR). [smaller MR indicates stronger coexpression]
• Column3: Pearson's Correlation Coefficient (PCC). [larger PCC indicates stronger coexpression]