How does Cufflinks determine Differentially Regulated Genes (relCDS)?

[jmwhitha]

Hello all,

I found something potentially interesting in my data where out of 1981 regulated genes (relCDS), just 1 was differentially expressed.

What I want to know is:

How does Cufflinks figure out what CDS's are regulated?

And, is there a way to discover the identity of the regulator?


This is what I found so far, but it doesn't answer my question:
"9.1 Creating gene sets from significantly regulated genes
One of the primary roles of a differential expression analysis is to conduct significance tests on each feature (genes, isoforms, TSS, and CDS) for appropriate pairwise comparisons of conditions. The results of these tests (after multiple testing correction of course) can be used to determine which genes are differentially regulated."
-http://compbio.mit.edu/cummeRbund/manual.html

God bless,
Jason

[jmwhitha]

Okay, so I must of missed these when I read the article.

"By grouping transcripts into biologically meaningful groups (such as transcripts that share the same transcription start site (TSS)), Cuffdiff identifies genes that are differentially regulated at the transcriptional or post-transcriptional level."

"Cuffdiff also reports additional differential analysis results beyond simple changes in gene expression. The program can identify genes that are differentially spliced or differentially regulated via promoter switching. The software groups together isoforms of a gene that have the same TSS. These TSS groups represent isoforms that are all derived from the same pre-mRNA; accordingly, changes in abundance relative to one another reflect differential splicing of their common pre-mRNA. Cuffdiff also calculates the total expression level of a TSS group by adding up the expression levels of the isoforms within it. When a gene has multiple TSSs, Cuffdiff looks for changes in relative abundance between them, which reflect changes in TSS (and thus promoter) preference between conditions. The statistics used to evaluate significance of changes within and between TSS groupings are somewhat different from those used to assess simple expression level changes of a given transcript or gene. Readers interested in further statistical detail should see the supplemental material of Trapnell et al."

And figure 4.

-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/

Does this mean that Cufflinks decides to call a CDS a "regulated CDS (relCDS)" if two or more transcripts of different lengths (caused by inter/intra transcriptional modification) are found in different abundances between samples? These are then analyzed differently than regular gene expression differences?