WORLD Sign In Sign Out

Help : Expresson Connection Help


What is ExpressionConnection?

Expression connection provides users an easy access to explore the entire clustered datasets from a given publication in TBDB. This way a user can directly view clustered datasets, explore and interrogate TBDB without going through data analysis pipeline. Expression connection also enables a user to search for expression data for a given gene in TBDB.

Accessing expression data:

Overall expression data can be accessed from a given publication using Publication Page or you can access gene-specific expression data using quick search feature.

How to access expression data from a Publication Page?

To access expression connection choose Gene Expression Publications from TB Expression pull down menu on tool bar. This will give a list of publications in TBDB. By clicking on Data in TBDB you will be taken to a publication page. Alternatively from tool bar select TB Expression Lists All Programs. This will list all available lists and options in TBDB. Click on publications under List Data to go to TBDB publications list.

View Publication Page

View Publication page provide an overview of all different options available for a given publication in the database. This page is organized into 3 sections. These consist of a Citation, Associated Links section and Associated Experiment Sets.
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.

Exploring ClusterImage

Exploring Cluster Image: This cluster image is generated using raw data in a given publication. The goal is neither to reanalyze the data nor to present an exact replication of authors analysis of a publication data. Rather aimed at providing a standard view of clustered data set. This will enable researchers to further explore data presented in a publication beyond the hypothesis put forward by authors.

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.

How to access gene-specific expression data?

Enter a gene of your interest in Quick Search field and click on search. Search results provide a link to Expression Connection page. Expression connection page lists all available publication datasets for the gene you searched for. For each dataset the following 3 types of information is provided.

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.