Dear Pantelis,

the isoform abundance analysis CON vs DOX for the combined runs 275,276 and 2 samples merged from run 288
has finished.
I have lifted the latest annotation from hg38 (GRCh38.84 of June 6) to hg19.

The following isoforms are significantly downregulated in DOX:
BRSK2	chr11:1411128-1483919
POSTN	chr13:38136719-38172981
FLYWCH1	chr16:2961937-3004277 (novel isoform)
SPDYE19P	chr7:5013618-5112854
MIR491	chr9:20658307-20995954

No significant upregulation in DOX was detected.
See the attached xlsx for all results.

http://genomics-lab.fleming.gr/fleming/PHlab/run276/cuffdiff_CON_vs_DOX/
Note that there are 81 significant deregulations at the gene level
and 13 significant deregulations for TSS groups
(see http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#cuffdiff-output-files).

BW,
Martin