Cuffdiff isoform_exp.diff output: How do you find which isoform TCONS id is referring to?

Question

[Yuka Takemon]

Hello!

I am analysing RNAseq data using cufflinks/2.2.1 to run cuffdiff for two groups of samples WT vs KO. I am interested in knowing which of the isoforms of a corresponding gene is differentially expressed.

test_id gene_id gene    locus   sample_1    sample_2    status  value_1 value_2 log2(fold_change)   test_stat   p_value q_value significant
TCONS_00005883  XLOC_003696 Myo1c   chr11:75651508-75674634 WT  KO  OK  0.695384    0.813635    0.226571    0.134985    0.7983  0.999954    no
TCONS_00005884  XLOC_003696 Myo1c   chr11:75651508-75674634 WT  KO  OK  2.70472 5.00692 0.888442    2.3638  0.0006  0.327444    no
TCONS_00005885  XLOC_003696 Myo1c   chr11:75651508-75674634 WT  KO  OK  65.5926 118.552 0.853912    3.30047 5.00E-05    0.0508103   no

I know that I should be looking at the TCONS id number, but which transcript is it actually referring to in relation to databases such as Ensembl? and how do can I look this up? In the above example for Myo1c, when you look this gene up on Ensembl there are 5 protein coding transcirpts, but there are only 3 in the cuffdiff output with different id systems.

I would appreciate your input.

Thank you,

Y

[fanli.gcb]

If you followed the Tuxedo pipeline, then I'd guess these are in the output from cuffmerge (e.g. merged.gtf). Some sample lines below:

chr1    Cufflinks       exon    788859  794826  .       +       .       gene_id "XLOC_000006"; transcript_id "TCONS_00000013"; exon_number "7"; gene_name "LINC01128"; oId "NR_047520"; nearest_ref "NR_047520"; class_code "="; tss_id "TSS6";
chr1    Cufflinks       exon    762971  763155  .       +       .       gene_id "XLOC_000006"; transcript_id "TCONS_00000015"; exon_number "1"; gene_name "LINC01128"; oId "NR_047522"; nearest_ref "NR_047522"; class_code "="; tss_id "TSS6";