A Spearman rank correlation test [ 26] was performed on each GO term vector and the upstream alignment score vector, in order to test whether each GO term is associated with high or low proximal upstream conservation.
Also, a high G+C% is indicative of a higher neutral substitution rate, due to a higher rate of mutation at methylated cytosines in CpG sites and some other factors [ 15, 16] We performed a partial rank correlation [ 17] between upstream alignment score and GO term label, controlling for G+C%, to eliminate the effect of G+C% in the correlation test.
First up is GroupMe's new gallery view — rather than forcing users to scroll upstream through scores of old messages in search of previously shared photos, the app now lets them view all those photos in one fell swoop.
Interestingly, more routine processes such as 'biosynthesis' and 'ribosome' turned out to be correlated with low upstream alignment scores (Table 1, 2, Additional file 1: Table 1).
For the Zelda motif, which can occur multiple times in a single promoter region, the presence of at least one motif within 2 kb upstream was scored.
To measure proximal promoter conservation, upstream alignment scores of human genes were computed by counting the number of matches in the alignment between the sequence 1 kb, 2 kb and 5 kb upstream of the transcription start site and its syntenic mouse sequence.
Each gene's upstream region is scored with matrix m by counting the number of randomly drawn genes that achieve scores equal to or greater than c m.
Our data confirm the implication of NAFTC2 in HT-29R CC cell line as an important upstream regulator (z-score = 3.019, p = 3.84E-05).
We identified functional categories that are enriched towards high proximal promoter conservation by computing a Spearman's rank correlation on upstream sequence alignment scores and Gene Ontology (GO) [ 11] terms.
For instance, in the experimentally defined transcriptional unit containing the genes deoC, upp, MHP7448_0525, lon and tuf, all the genes, except MHP7448_0525, contain promoter sequences in their upstream regions (with scores varying from 8.4 to 11) (data not shown).
