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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___________________________________________________________
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