Analysis for Differentially Expressed Genes (DEGs)a.

aTranscripts were grouped by various combinations of analysis into three columns: Total Assembled transcripts; RefSeq - transcripts matching or partially matching RefSeq genes; and Novel transcripts. In the first row, Total CuffCompare transcripts included all transcripts (57,076); RefSeq transcripts (complete or partial match) were 45,144 (14,257+30,887 = 45,144); and 11,932 potentially novel transcripts. Note, that a set of 1,496 Cufflinks assembled transcripts referred to as, ‘Others’, contained significant repeat sequences and so this small set of transcripts was excluded (e.g. –‘Others’) from Total Assembled transcripts. In row 2, to enable comparison with available Microarray data, we identified Cufflinks assembled transcripts that overlapped MA probes (total 44,469 transcripts). From this group of transcripts, we determined differential expression (DEGs) using student’s t-test in the case of MA (microarray) data in row 4, or for RNA-Seq data we performed DESeq analysis in row 3 or Cuffdiff analysis in row 5 (see Materials and Methods for details).