RiceXtra

Help

How to use the tool:

  1. Go to the tool section.
  2. In the search panel click the option you want to check.
  3. Write the MSU ID (with splice variant Eg. LOC_Os00g00000.1) you want to check and submit.
  4. For batch search, enter "n" IDs separated by (space or comma or return)

Details provided by different lists:

Affymetrix microarray: Relative fold change of rice genes in various experiments following treatment with Xanthomonas when the analysis was performed using Affymetrix microarray platform (Transcriptome Analysis Console, TAC ver 4.0).

RNA-Seq: Relative fold change of rice genes in various experiments following treatment with Xanthomonas when the analysis was performed using RNA sequencing analysis pipeline (usegalaxy.org/Galaxy server).

Elicitors of immunity: Relative fold change of rice genes in various experiments following treatment with either lipopolysaccharide or cell wall degrading enzymes when the analysis was performed using Affymetrix microarray platform (Transcriptome Analysis Console, TAC ver 4.0).

Inference Affymetrix/RNS-seq: A general inference of a gene expression pattern in all the analyses performed in this study.

  • No. of experiments in which the gene is differentially expressed
  • No. of experiments in which the gene is up regulated
  • Fraction of the times the gene is upregulated. Genes that are mostly up regulated after Xanthomonas treatment have an up regulation ratio (U/C) close to 1, while the genes that are generally down regulated have U/C close to 0.
  • Affymetrix: More than 1 row indicates multiple probes that detect the gene of interest.

ID converter: Convert RAP or Affymetrix gene chip ID to MSU ID.