Hi Wei,

BioMart has tools to extract tabular data that maps Ensembl transcript identifiers to alternate identifiers, gene symbols, etc. See the tool under "Get Data -> BioMart Central server". You'll likely have to map from Ensembl transcriptID -> HGNC transcript -> HGNC gene


http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000223972;r=1:11872-14412;t=ENST00000515242

Other sources also have this type of data:
http://www.genenames.org/data/hgnc_data.php?hgnc_id=37102

The Cuffdiff file will also need to be prepared, the Ensembl transcripts need to be in tabular format. 'Convert Delimiters to Tab' is the correct tool choice.

Then, once both files have the data you wish to you in tabular format, join the data on common keys using tools in 'Join, Subtract and Group -> Column Join'.

To finish, use tools in 'Text Manipulation', 'Filter and Sort', and 'Join, Subtract and Group' to format the data so that it is useful for your purposes.

If you need help, we have screencasts cover most of these text manipulation operations: Galaxy 101 + Tool tutorials (top 6)
http://wiki.g2.bx.psu.edu/Learn/Screencasts

Hopefully this helps,

Jen
Galaxy team

On 4/19/12 1:43 PM, Wei Liao wrote:
Hi all,
I had the following Cuffdiff output from genes defferetial expression
testing:
test_id         gene_id         gene    locus   sample_1        sample_2        
status  value_1
value_2         log2(fold_change)       test_stat       p_value         q_value
XLOC_000001     XLOC_000001
ENST00000450305,ENST00000456328,ENST00000515242,ENST00000518655
chr1:11868-31109        NORMAL  1       OK      0.558797        0.84004         
0.588134        -0.44598
0.655611        0.767628

There are four transcript IDs belong to gene DDXL11L1, my question is
how to replace these ID with official gene names?
Thanks,

--
Wei Liao
Research Scientist,
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645



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