The automated gene assignments by HOMER can arbitrarily assign peaks to one of two divergently transcribed genes, although the distance of RBf peak to the more distal TSS may be close enough to be functionally important.
With two grapevine genome sequences completed [ 1, 2] the non-trivial task of identifying and assigning biological functions to the putative gene assignments begins [ 3].
Of these, 17,259 terms (assigned to 13,070 genes) are molecular function, 8,864 terms (7,111 gene assignments) are biological process, and 3,650 terms (3,257 gene assignments) describe cellular component.
Replicates were transformed to log2 normalised mean expression (NME), and gene symbols were assigned using the mouse4302.db library in R. Using the background gene assignments from section 'GO Analysis', 1000 genes were drawn at random, and the median of each tissue/cell expression profile for these genes was calculated from the NME of all samples.
However, in several cases, the number of genes assigned to a grouping was small in number, and often with an absence of gene assignments within 1 of the 2 cells being compared.
(In other obligate oxidative bacteria, orthologous gene assignments are variant, e.g. hoxKG in R. eutropha [12]).
Gene assignments and expression data were extracted using the DeArray Suite [38] for IPLab spectrum.
An additional 1,673 probes were found to have dubious gene assignments (due, for example, to identical matches to multiple genes).
Putative chicken Smad6 and Smad7a and Smad7b gene assignments were made based on similarities of the predicted protein sequences with published family members and sequences submitted to Genbank.
While the molecular coordinates of each insertion site is known, gene assignments are sometimes ambiguous, as the modifying transposon may have inserted between two genes.
Despite the essential role of SMN in snRNP assembly [12], an unexpected result of the screen was that none of the modifying insertions for which unambiguous gene assignments were made appear to function in RNA processing.
