Input Data Format

Plant MetGenMAP takes normalized and processed expression and metabolite profile data (mainly ratios and p values derived from statistical analysis programs such as LIMMA and SAM) as the input. Users can upload expression profile data and the metabolite profile data to the system separately or simultaneously. Each uploaded dataset must be in a specific format in order for it to be compatible with Plant MetGenMAP. All datasets must be in tab delimited plain text file format. The first line of the dataset must contain the labels including ID, condition names, and p values (if available) for each sample in the dataset.

ID - Unique identifier for each gene or metabolite included in the dataset. For gene expression dataset, the ID must be in one of the formats specified under ID type in the upload form. For metabolite profile dataset, the ID is the name of each metabolite.

Note: All available synonyms of metabolite names were collected from the corresponding BioCyc databases. A file containing these synonyms is provided on the website. The system accepts synonyms of metabolite names and converts them to metabolite common names. When preparing metabolite data, please make sure the metabolite names are consistent with the names/synonyms listed in the file.

Condition/comparison Name - The name of conditions or comparisons under which the data (ratio or fold change) was derived. The condition/comparison names must be unique across the same dataset.

P value - Statistical value of probability. This is optional.

Here is an example of datasets with p values

Example: ID[TAB]blue light[TAB]p value[TAB]red light[TAB]p value[TAB]white light[TAB]p value 254685_at[TAB]-45.7[TAB]0[TAB]-19.29[TAB]0[TAB]-11.89[TAB]0 263151_at[TAB]-1.89[TAB]0[TAB]-1.15[TAB]0.83[TAB]-1.24[TAB]0.36

Here is an example of datasets without p values

Example: ID[TAB]blue light[TAB]red light[TAB]white light 254685_at[TAB]-45.7[TAB]-19.29[TAB]-11.89 263151_at[TAB]-1.89[TAB]-1.15[TAB]-1.24

More example input files can be found on the site.

Note:There is no limit to the number of conditions/comparisons or p values included in a dataset. However, datasets with p values must have p values for all conditions/comparisons within the dataset. In addition, corresponding expression and metabolite datasets must have the same header and format.