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majority genes being expressed highly in normal lung is not evident from data

Posted by mnandita on 05 Nov 2009 at 05:30 GMT

we found that the majority of genes were on average expressed at higher levels in the normal samples.
http://plosmedicine.org/article/info:doi/10.1371/journal.pmed.0030486#article1.body1.sec3.sec4.p2

As per data in table S3, it seems like only 50%, and not a majority of the 94 significantly differentially expressed genes between tumor and normal are expressed at higher levels in the normal samples. (fold difference of geom. means < 1)

Competing interests declared: I am a lung cancer researcher and trying to mine the data in this paper for further studies

RE: majority genes being expressed highly in normal lung is not evident from data

dsshames replied to mnandita on 16 Nov 2009 at 22:13 GMT

The sentence referred to in this comment addresses figure 5, whereas the author of this comment has incorrectly assumed Figure 5 is derived from the supplementary table S3. The text clearly states:

After extracting the relevant probes and filtering the data, we found that the majority of genes were on average expressed at higher levels in the normal samples. While marked gene expression differences between NSCLC and normal lung are to be expected, the 5-aza induction gene set clearly distinguished these phenotypes in our data (Figure 5).

i.e. the “majority” of genes we refer to is in figure 5, as demarked by the dendogram on the vertical axis. Thus the data in figure 5 do support the use of the word majority. However, the next sentence, which refers to Table S3 and where we make no mention of a “majority” of genes, simply states that 94/117 were differentially regulated by SAM:

Of 117 unique genes in this group, 94 were differentially expressed between tumor and benign tissue based on the SAM algorithm (90th percentile confidence, false discovery rate among the 94 significant genes was 0.11 and the delta value used to identify significant genes was 0.54) (Table S3).

No competing interests declared.