CuffDiff Output Interpretation

Question

[Light]

These are the output of cuffdiff

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 XLOC_000009 XLOC_000009 NM_005101 chr1:1013466-1014539 infected Normal OK 1025.95 5.54585 -7.53133 -15.7114 5.00E-05 0.000259058 yes XLOC_000010 XLOC_000010 NM_001305275,NM_198576 chr1:1020122-1056119 infected Normal OK 159.971 45.0202 -1.82917 -7.42355 5.00E-05 0.000259058 yes

In some gene_id column, there are multiple entries. Does it means that these genes are expressed with same fold_change value?

Answer 1

[BioinfGuru]

The entry in the gene_id column refers to the accession number/s associated with the entry in the gene locus column

Each XLOC is a single transcript found in both samples (infected + normal) .... For XLOC_000010, the gene locus chr1:1020122-1056119 has been previously annotated in the refseq database with the mRNA accession numbers NM_001305275 and NM_198576. These are simply transcript variants.

https://en.wikipedia.org/wiki/Agrin

... look on the right in the ortholog box under " refseq"

... you'll find your to NM accession numbers there

... click the links to see what they are.

To put it more simply, 2 different labs have annotated this locus .... so (for reasons not needed here) it has 2 geneIDs, thats all.....you can ignore it regarding fold change

log fold change = log2(value_1) - log2(value_2)

NB: As a point of advice, I suggest you focus on test IDs (the primary key) and only at the end when you have found something interesting, then pull out the "geneID" for more information about the transcript (and its variants)