Find Transcriptome Signatures with TranscriptomeBrowser
Search public GEO datasets, identify specific transcriptome signatures, and perform functional enrichment on the found sets
TranscriptomeBrowser (TBrowser) host a large database of transcriptional signatures (TS) extracted from GEO public microarray repository . TS have been produced using a new algorithm called "Density Based Filtering And Markov Clustering" (DBF-MCL). The current database contains about 30 000 TS derived from ~ 4 000 microarray datasets (~222 millions expression values). Each TS was tested for functional enrichment using annotation obtained from numerous ontologies or annotation databases (Gene Ontology, KEGG, BioCarta, Swiss-Prot, BBID, SMART, NIH Genetic Association DB, COG/KOG, TargetScan, PicTar, .TFBS_conserv.ed., MSigDB, GeneSigDB,...). TBrowser comes with a sophisticated search engine so that users can perform combined queries using boolean operators.
VERSION 3.0. TranscriptomeBrowser host a large database of transcriptional signatures (TS, n~40 000) extracted from Gene Expression Omnibus (~4 000 experiments) using the DBF-MCL algorithm. TBrowser comes with a sophisticated search engine so that users can search for the biological contexts in which several genes were concomitantly regulated. Several examples are provided below and in the article published in PLoSONE . A video tutorial for TranscriptomeBrowser is available here and a second for the InteractomeBrowser plugin here. The full manual can be read here
After installation (see online documentation) and startup, the main TBrowser interface awaits user input
A Walk-through example
As shown above, different search angles can be used to populate the interface. Instead of searching for genes, we choose to use here the GSE6943 dataset used in other BITS training tutorial(s). Please refer to the Hands-on_Analysis_of_public_microarray_datasets page for more information about this dataset.
Load the GSE6943 dataset
Change focus to search for 'Experiment' and type GSE6943 in the text field followed by a click on 'SEARCH'
Four enriched TS (Transcriptome Signatures) are found by the program
Several options are available here (please explore) and we choose to show the results to get details about the four hits
Find Transcriptome Signatures
Selecting each of the four hits and displaying the detailed statistical results on the top-right window
- first TS (662 genes) and Glycolysis as main aspect
- second TS (778 genes) related to mitochondrial functions
- third TS (622) clearly associated with heart and mitochondrial functions
- last TS (684) apparently specific to the cardiac muscle
Show HeatMaps for each TS
For each TS, we can visualize the actual expression data as a heatmap by using the corresponding plugin
- first heatmap (cut at ~20 genes)
the leftmost 6 samples are the Diaphragm replicates while the remaining ones are the Heart replicates
The full heatmap picture can be saved to file using buttons present at the bottom of the window
- second heatmap
- third heatmap
- fourth heatmap
And there is even more for Geeks
The data mining package, RTools4TB, can perform calls to TranscriptomeBrowser web service and implements the DBF-MCL algorithm. The R package RTools4TB is now part of the Bioconductor project.