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Table 2 Novel transcripts detected by Cufflinks/Cuffmerge/CuffDiff pipeline

From: Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines

Name Location Fold change (case/control) Corrected p value Spliced? Histone mark? EST?
CUFF.11349 chr8:101524720-101588587 -1.88185 0.041685 Yes Yes Yes
CUFF.2472 chr12:31838565-31853772 -2.26342 0.123977 Yes Yes Yes
CUFF.3 chr1:80691-80824 -11.5273 4.46E-08 No Yes Yes
CUFF.4 chr1:452495-461228 -10.6557 7.54E-10 Yes Yes Yes
CUFF.5* chr1:163653-164729 -12.5567 1.96E-10 No No Yes
CUFF.6* chr1:164811-166159 -12.8975 1.27E-12 No No No
CUFF.7* chr1:166235-166948 -12.7567 1.27E-12 Yes No Yes
CUFF.9 chr1:227665-257075 -11.1513 1.18E-08 Yes Yes Yes
  1. Column 5 denotes presence of spliced reads following GT-AG rule. Column 6 denotes presence of layered H3K4Me1 or H3K4Me3 histone modification marks at the locus. Column 7 denotes the presence of spliced or unspliced human ESTs in the UCSC Genome Browser database. *CUFF.5, CUFF.6 and CUFF.7 were annotated by the Cufflinks pipeline as separate transcripts but their close location suggests that they may be components of the same transcript.