What does the “log2(fold change)” in the gene differential expression testing result

[seqprone]

What does the “log2(fold change)” in the gene differential expression testing result mean?

A) Its the log-ratio of FPKM values for a pair of expressed genes.
B) Its the log-ratio between mapped and unmapped reads.
C) It indicates genes with significantly different expression profiles.

I thought it was C but it turned out to be wrong. Please help!

[dpryan]

A fold change is, by definition, a ratio, thus it can't be C. While one could look at the ratio between mapped and unmapped reads, that wouldn't make any sense in terms of differential expression, thus it can't be B. Consequently, it must be A, which is one was of getting a log2FC, though in reality one shouldn't use FPKMs (that will hopefully be a different lecture).

[Michael.Ante]

Hi seqprone,

The log2(fold-change) is the log-ratio of a gene's or a transcript's expression values in two different conditions.
While comparing two conditions each feature you analyse gets (normalised) expression values. This value can be zero and thus lead to undefined ratios.
The differential expression is computed with a statistical test including not only the ratio but also the variance in the samples and other parameters.
Cheers,
Michael

[seqprone]

Thank you for the answers!

unfortunately, I still didn't get the right answer.

Both A and C are wrong =(

for the question :

What does the “log2(fold change)” in the gene differential expression testing result mean?

A) Its the log-ratio of FPKM values for a pair of expressed genes.
B) Its the log-ratio between mapped and unmapped reads.
C) It indicates genes with significantly different expression profiles.


The answer options are:

A
C
A and C
B

Since both C and A are wrong, I'm left with either (B) or (A&C).

If it helps, the data we're talking about is Cuffdiff output (in tabular format) as generate by Galaxy as given below.

test_id XLOC_000001
gene_id XLOC_000001
gene -
locus chr1:224139222-224139367
sample_1 CD20
sample_2 H1hesc
status OK
value_1 15194.90
value_2 1391.60
log2(fold_change) -3.44877
test_stat -49.5206
p_value 0.0508
q_value 0.0820411
significant no

[dpryan]

Presumably whoever made the test mistakenly believes the answer to be "A and C". Note that that's actually wrong. Whoever wrote the test doesn't know enough to have done so.

[seqprone]

Ok! I'll try A&C but as a concept, I'll keep what you said in mind. It's one thing to score on a multiple choice quiz and another to know the 'right answer'. Thank you so much again for your help!