Segmentation Tables Legend

These tables list the segments resulting from the segmentation of the probe-response normalized hybridization signal along genomic coordinates. The segments are ordered by the category they were assigned to. Each row holds the information for one segment. The columns are as follows:

plot

links to the along-chromosome plot (in jpg and pdf format) containing the segment

segID

unique integer identifier for each segment. The counting starts at 1, corresponding to the most 5' segment on the "+"-strand of chromosome 1.

chr, strand

chromosome and strand

start

coordinate of the first base of the first probe belonging to the segment. The coordinate system is such that 1 is the 5' terminal base of the chromosome's "+" strand. Note that start corresponds to the 5' end of a segment if it is on the "+" strand, and to the 3' end if it is on the "-" strand.

end

coordinate of the last base of the last probe belonging to the segment. Note that end corresponds to the 3' end of a segment if it is on the "+" strand, and to the 5' end if it is on the "-" strand

length

end-start+1

frac.dup

fraction of probes with multiple hits in the genome (aka "non-unique probes")

level

mean expression level over all unique probes in the segment

category

categorization based on overlap with annotated genomic features and level. If a segment overlapped multiple genomic features, in order to assign it to a single category, a trumping order was used as described in the paper.

verified gene

segment overlaps a verified ORF

uncharacterized gene

segment overlaps an annotated but uncharacterized ORF

dubious gene

segment overlaps a dubious ORF

pseudogene

segment overlaps a pseudogene

transposable_element

segment overlaps a transposable element

rRNA

segment overlaps a ribosomal RNA

snoRNA

segment overlaps a small nucleolar RNA

snRNA

segment overlaps a small nuclear RNA

tRNA

segment overlaps a transfer RNA

ncRNA

segment overlaps a non-coding RNA

repeat_region

segment overlaps a genomic region containing tandem repeats

unannotated isolated - filtered

segment does not overlap any annotated genomic feature and meets the filter criteria (see manuscript and supplementary material)

unannotated isolated - unassigned

segment does not overlap any annotated genomic feature and does not meet the filter criteria.

unannotated antisense - filtered

segment does not overlap any annotated genomic feature on same strand but is located opposite to an annotated ORF on the other strand. In addition, it meets the filter criteria.

unannotated antisense - unassigned

segment does not overlap any annotated genomic feature on same strand, but is located opposite to an annotated ORF on the other strand. It does not meet the filter criteria.

excluded

due to too many non-unique probes the segement was excluded from further analyses

untranscribed

segment was not measured as being transcribed

overlap

percentage of annotated (SGD) genomic feature that is overlapped by the segment.

overlappingFeature

names of genomic features, on the same strand, overlapped by probes in the segment

oppositeFeature

names of genomic features on the opposite strand facing probes in the segment

utr5, utr3

number of bases in the segment exceeding the 5' (resp. 3') end of an annotated ORF, this is used as the estimate for the length of the 5' (resp. 3') UTR. Only exists if the segment overlaps an annotated ORF and the segment boundary meets filter criteria. Otherwise, it is NA (Not Available).

z3, z5

z-scores for the 3' and 5' flanks of the segment. They are calculated as the difference between the segment's level and the mean of the signal from the 10 neighboring probes immediately next to the segment, but fully outside, divided by their standard deviation. If the 10 probes would reach beyond the neighboring segment, this number is reduced so that all probes are within the neighboring segment. Note that the standard deviation of the signal within the segment is not considered here.

featureInSegment

annotated genomic features fully contained in the segment

mostOfFeatureInSegment

annotated genomic features contained to more than 50% in the segment

overlapFeatAll

genomic features partly or fully contained in the segment

oppositeExpression

mean expression level over all probes on the opposite strand of that segment. NA (Not available) in the case that on the opposite strand there is less than one full probe located between segment start and end position