Hi Vaibhav, In order to obtain a list of tissue specific genes, please see this answer from a previous question (substitute rn4 where it says hg18): https://lists.soe.ucsc.edu/pipermail/genome/2006-September/011685.html
We don't currently have a track with transcription factor binding sites for rn4. However, you may find the TFBS Conserved track on the hg18 human assembly useful. This track contains some rat transcription factor data. The track description is here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=tfbsConsSites. You can obtain a list of the rat transcription factors that are in the TFBS conserved track along with their hg18 coordinates using the table browser (click "Tables" on the top blue menu bar). Select the Human Mar. 2006 (NCBI36/hg18) and make the following selections: group: Regulation track: TFBS Conserved table: tfbsConsSites filter: click 'create'; under Linked Tables (bottom of page), select "hg18.tfbsConsFactors" & click "Allow filtering Using Fields in Checked Tables"; where you see 'species "does" match' delete the * and enter 'rat' (without quotes); click submit. output format: selected fields and related tables output file: since there will be a lot of results, enter the name you would like an output file to have file type returned: plain text Click "get output". Under Linked Tables, select 'hg18.tfbsConsFactors' and click "Allow filtering Using Fields in Checked Tables". select all the fields from both tables except 'bin' and click 'get output.' If you want to convert these rat TFBS coordinates from hg18 to rn4, you can do most of the same directions as above, but set the 'output of format' to 'BED - browser extensible data' and enter a new file name. Then you can use the liftOver utility (http://genome.ucsc.edu/cgi-bin/hgLiftOver) to convert the hg18 coordinates to rn4 coordinates. However, because file is so large, rather than using the web version you'll need to download the liftOver executable (http://hgdownload.cse.ucsc.edu/admin/exe/) and necessary chain file (hg18ToRn4.over.chain.gz from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/). For more information on using the liftOver executable, please see this previously answered Mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2008-August/016898.html For a list of the rat transcription factors from the TFBS conserved site without hg18 coordinates, you can make the same selections in my original directions, but for table select tfbsConsFactors. Filter that table the same way I described above, and after clicking get output, select your fields interest and sumbit. I hope this information is helpful. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group vaibhav jain wrote, On 01/13/11 23:53: > Hello everyone > I want to retrieve Transcription factors and the regions to where they bind > for Rattus novericus of rn4 assembly. Is it available in UCSC ??? Also I > want to retrieve liver specific genes again for Rattus novergicus and same > assembly. So can I get both these things from UCSC ?? Or should I look for > them on other databases or through literature ??/ > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
