Biological Pathways

Display expressions from transcriptomic or proteomic studies using MapManJS.

Gene and protein expression data can also be viewed over biological pathways using this instance of MapManJS, a web-based implementation of MapMan.

Assembled transcipts or protein sequences were aligned by Reciprocal Best Hit against cs10 mRNA or protein, respectively. cs10 mRNA or protein are then aligned by Reciprocal Best Hit with A.thaliana mRNA or protein, and displayed on the MapMan pathways for A.thaliana. Mapping through E. grandis and S. lycopersicum genes are also available. The expression data are from the Expression Viewer module.

1. Pathways - select pathway to display
2. Mapping - select cs10 to MapMan organism pathway mapping to use
3. Expression experiment - source of expression data/publication
4. Display value - value to display, blue means >0 and red means <0. For experiments with absolute expression values, the user can opt to display either the absolute value or the log2 ratio between two samples by selecting the sample in tthe numerator and reference in the denominator. Some experiments only have log2 fold change data available, for these the denominator option should be set to 1.