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Searching the Gene Expression Atlas
This help page provides information about:
Simple searchesWhen you search the atlas, you provide some general query parameters:
The first parameter will identify all genes whose annotation matches your query. The second and third parameters restrict your search only to genes belonging to a given organism and also by direction of differential expression: up or down. See details of Atlas construction for further information concerning the meaning of "up" and "down" in the Atlas context. The fourth parameter will identify all experiments in which conditions, e.g. disease or tissue, that match your query appear. Any of the genes, organism or conditions boxes can be left blank but not all three. Leaving the gene selection blank will apply your condition query to all genes in the Atlas; leaving the conditions textbox blank will rank the genes found for differential expression across all conditions in the Atlas. Multiple values can be entered into the gene and condition search boxes. Separate each by a space. This will be treated as an 'OR' connecter. E.g. entering 'liver kidney' in the conditions box will find genes expressed in liver OR kidney. AutocompleteThe gene and condition boxes have autocomplete functions. The gene autocomplete groups autocompleted hits together by gene and list general textual hits (e.g. GO categories below). To select one of the suggested values click on the value in the list. If you do not want to select any suggested value click on 'Hide suggestions'. The condition box uses a controlled vocabulary called EFO to expand queries, query synonyms and to suggest query terms. Gene autocomplete
Condition autocomplete
See also Advanced searchesThe advanced search allows you to restrict your search by specific gene and condition properties. To use the advanced search, click on the 'advanced search' link below the simple search box.
Build up complex queries by adding condition (experimental factor), gene property and organism filters one by one. E.g. the following query will search for genes from any organism that match the name MAT1A, such that they are over-expressed in liver and over- or under- expressed in adult animals. Each additional row acts as an 'AND' in the query. Entering more than one value in each row acts as an 'OR' in the query. e.g. the following query will search for genes from any organism that match the name MAT1A OR CYP1A1, such that they are over-expressed in liver OR kidney and over- or under- expressed in adult animals.
You can also search for phrases in quotes, e.g., "cell adhesion" or "non-small cell lung carcinoma", in any input field to search for all phrase matches in the Atlas. Search phrases can be combined with keywords, separating search terms with spaces. For example, the query might be: "cell adhesion" apoptosis. This will search for any terms matching "cell adhesion" or apoptosis. Linking to the AtlasYou can link directly to information about the expression of genes in the Atlas using certain gene identifiers and Gene Ontology (GO) terms in a URL link. See the help page on Atlas links for more information. Results display - heatmap viewIf your query matches more than one gene then the results will be displayed in a heatmap. E.g. a search for gene 'MAT1A' with no organism specified will give the following result.
Each row of the result table corresponds to one gene's (or probe) differential expression from the Atlas. The complete description of all displayed fields is as follows:
Clicking on a cell in the heatmap will show more information about the expression of the gene in the experiment(s). For example a search for gene MAT1A in experiments with condition = liver gives the following result and clicking on the cell with the number 2 in it gives the following window:
Results display - gene viewIf your search returns hits for one gene only, or you click on one gene from the gene list returned from a broader search a gene page will be returned. The gene view provides a one-page summary of Atlas information about a given gene, it's annotation and summaries of expression from different experiments.
E.g. the human gene MAT1A shows the highest level of differential expression in the experiment E-AFMX-5. It is over-expressed in liver. Clicking on any of the factor values in the left hand list will only showexperiments where this gene is over- or under-expressed in selected condition. Clicking on the "expression profiles" link will take you to the expression profile for the gene in the selected experiment.
Additional resources
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The Gene Expression Atlas is essentially a two-dimensional matrix where rows correspond to genes, and the columns corresponds to conditions such as compound or disease state. The matrix entries are p-values together with a sign, indicating the significance and direction of differential expression. See 
