- The heatmap is a way of representing the data that we will encounter many times across the Atlas. It is the default output when searching the Atlas by condition [A]. The heatmap is nothing else than a table, where each row represents a gene, retrieved by your search, and each column is a condition in which the gene was detected as differentially expressed. An entry in the table shows how many times the gene was detected as differentially expressed in the corresponding condition. The colour of the cell (or part of the cell) indicates whether the gene is over- or under- expressed. A white cell (or part of the cell) indicates in how many experiments there was no change in the gene expression; please note that the experiments where there was no change in the gene expression are not shown by default. In the example, ‘Gene A’ was observed over-expressed in ‘Condition 1’ in 26/no change in 10 experiments and under-express in ‘Condition 2’ in 6 experiments/no change in 9 experiments. In the gene summary page [B], the heatmaps look slightly different and are split by condition. If you look at a gene summary page, you will find several heatmaps, one for each condition in which the gene was identified as differentially expressed (by default only the heatmaps for the first 6 conditions are show). Each heatmap will be a table with 3 columns: the first column listing all the values for the selected condition (e.g if the condition is ‘Cell line’, its values will be different types of cell lines), the second columns indicating if the gene was over- or under- expressed in the selected condition and in how many experiments and the third column listing the identifiers of these experiments.