TetraFGD Search Help

Currently, the Tetrahymena functional genomics database (TetraFGD) contains three major resources:

1) RNA-Seq data;

2) Microarray data;

3) Gene network.

We have supplied the search functions to access these data.

Integrated search

In any page of TetraFGD website, your can enter your gene ID (eg., TTHERM_XXXXXXXX), gene annotation or transcript ID from the RNA-Seq data to search the database through the top search box, leading to an integrated search results page that links the three major resources. Since the microarray platform was designed using the 2006 version of the Tetrahymena genome annotation, the gene ID and gene annotation in this version of genome annotation were used in the integrated search. A look-up table for conversion among 2006 genome annotation IDs, 2008 genome annotation IDs, transcript IDs and gene descriptions could found in Gene/Transcript ID page.

Specific search

Search RNA-Seq data: TetraFGD currently display the RNA-Seq data through Gbrowse (http://gmod.org/wiki/Main_Page). The Tetrahymena 2008 version of genome annotation was used for the RNA-Seq data, thus, Gbrowse currently only supports the gene ID and annotation in the 2008 version. We strongly suggest you use the TTHERM_XXXXXXXX ID to search Gbrowse as this type of ID did not change when genome annotation was updated. However, you can also use other information such as gene annotation, transcript ID or scaffold region (format like scaffold_x:position1..position2) to search in the Gbrowse “Landmark or Region” textbox. Gbrowse now has four tracks, including the 2008 gene predications, the RNA-Seq assembled transcript, the coverage plot and microarray probes. If you click the gene in the 2008 gene predication track, two hyperlinks will link you to TGD and the TetraFGD microarray data; if you click the transcript in the RNA-Seq assembled transcript track, a hyperlink will link you to the renormalized microarray data of transcript and its sequence. If you want to retrieve the sequence of a region, enter the region in the Gbrowse “Landmark or Region” textbox, and choose the “Download Decorated FASTA File” in the pulldown box, then excute “GO”. If you want to use the image of the Gbrowse to publish, just click “File” in left of the top, and “export as” the “editable SVG image”, then you can use Inkscape or Illustrator software to edit the image.

Search microarray: TetraFGD currently contains the microarray data of 20 time points of Tetrahymena life cycle. In the Microarray page, you can enter a gene ID to search the microarray expression profile, and can view the expression value by clicking the button “Value Table=>”. Since, according to our RNA-Seq data, many Tetrahymena gene models are mis-predicted, the microarray expression values of the assembled transcripts were renormalized using signals from probes reassigned to the corrected gene model. Therefore, you can also search the microarray expression profile by the transcript ID.

Search Gene network: Tetrahymena gene network (TGN) supplies an important resource to retrieve possible functionally related genes. TetraFGD currently contains the Tetrahymena gene network inferred by the CLR algorithm (http://gardnerlab.bu.edu/data/PLoS_2007/) which based on the mutual information other than the previous used correlation methods such as pearson correlation. We have filtered some low information content genes by microarray expression values, and 15,091 genes were used to construct the gene network. Therefore, some genes were not included in current TGN. In the Gene network page, you can enter one ID for “Single-Search”, this will get all the genes connected to your query gene in the TGN, and your can save it as text file. You can also enter several IDs to “muti-search”, the “muti-search” results will retrieve all the connections ( gene to gene, edges in TGN) among your supplied genes (note: some genes your supply will not be included in TGN because of our filter strategy), and the search results can be downloaded as a TAB separated text file that can be viewed using the Cytoscape software (http://www.cytoscape.org/).

Blast search

The RNA-Seq data have significantly improved the Tetrahymena thermophila gene models. We have assembled the transcripts using the RNA-Seq data. You can search the transcript sequences using nucleotide sequences by BlastN, or search the protein sequences by TBlastN. Also, you can use Blast search to find the transcript ID as these IDs have never been released before.