- What is ExpressionConnection?
- Accessing expression data
- How to access expression data from a Publication Page?
- View Publication Page
- Exploring Cluster Image
- How to access gene-specific expression data?
The first section provides citation, publication title, author names and abstract. This citation section can be toggled between full view displaying title, authors and abstract or just a citation by using the triangle button on the left hand side of the citation.
The second one is Associate Links section, which provide access to Full Text Online, PubMed Link, Web Supplement, Repositories like GEO and/or ArrayExpress and Publication Meta Data.
The third section lists the names of associated experiment sets for a given publication along with various options available to explore and analyze the datasets. Icons/Links appearing under options provide a link to these available options. Mouseovering on these icons provide more details about the link. These options include view cluster image, view data retrieval and analysis summary, view experiment set details, display data, data retrieval and analysis, data for individual sample, and down load raw data set.
The search box in the toolbar enables a string search of either all, or specific gene annotation fields presented next to a cluster image. The string may contain more than one term, where each term in the search string should be at least 2 characters long. Spaces between the terms are interpreted as term separators and the terms are combined using the logical 'AND' operator. For example a search for trans reg will return genes whose name contain transcriptional regulator etc. Wildcard searches are allowed using the '*' character, such that at least one character should precede the wildcard character. The hits resulting from the search are displayed in the zoom frame, as expression patterns. The number of hits displayed in the zoom window is limited to 200 hits.
The radar image on left hand corner can be used to zoom into a particular are of interest for detailed cluster image view. Width of the radar image can be changed from 50% to 400% using pull down option in tool bar.
Mouseovering on experiment name or on a row in cluster image will display corresponding info in text box on top.
By clicking on a cluster image row, a new image will be drawn for 20 most correlated genes, with the gene you clicked on will be placed at top. The genes with expression patterns similar to the gene of interest are presented in an ordered list. The length of the orange bar to the right of the expression data indicates the magnitude of the correlation value. By mouseovering on this orange bar will display the correlation values in text box on top.
By clicking on the blue link of a gene id next to a cluster image, will take you to a page displaying more details and links to other resources for this gene.
1. Experiment set detail: This section provides details of the experiment set.
2. Expression pattern for experiments: This section provides a link to gene explorer view of cluster image. Besides the gene of your interest it contains the next 19 correlated genes. This gene explorer image can be explored further as described above.
3. Log (Base2) ratio for experiments: Gene expression log ratios for all the experiments in the data set were shown in a histogram. You can sort the histogram by log ratios or experiment name. Mouseovering on a bar will display experiment name.