Exact(1)
For 4601 transcripts with reliable annotation (see Materials), the gene expression measurement according to the probes in the annotated direction was highly correlated to the number of reads produced by the sequencing.
Similar(57)
c Orthologous sequence present, but ORF annotated in reverse direction.
In GRNs the nodes are genes and the edges are influences, annotated with a direction and signed strength.
If one of the two signature sets is directional and the other is not directional, the overall score is represented by the larger of the two subset pair scores, annotated with the contributing direction from the directional signature.
The reaction is annotated with the reaction direction and if it is reversible or not.
In all the strains the gene before the USP was in the opposite transcription direction and annotated with function "Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)" [COG1028].
Explanation for DEGs with higher expression in the non-stranded data compared to the stranded data is not as straightforward but scrutiny revealed three dominant reasons for these DEGs; i) the DEGs have overlapping features that are unnannotated, ii) the DEGs are annotated in the wrong direction or iii) the DEGs have antisense intronic transcripts that get wrongly assigned to them.
When they're not, then diaries, letters, annotated drafts and stage directions are all really helpful to get the clearest sense of what the playwright envisaged.
All that remains of that presentation are Kandinsky's conceptual watercolors and a score used by the pianist Felix Klee (the son of the painter Paul Klee), annotated by Kandinsky with directions and durations to link the music with the staging.
We began with all noncoding loci (not contained within the coordinates of coding sequences as reported in version 3.1 of the D. melanogaster genome) that were at least 5 kb from annotated genes in both directions, as measured from the midpoint of the noncoding locus to the edge (5' or 3' end, depending on the genic orientation) of the nearest coding sequence.
Our deep dataset allowed us to identify 2710 clusters of small RNAs that overlapped annotated 3' UTRs in a sense direction (see Methods; a list of testis piRNA clusters that overlap with 3' UTRs is in Additional file 2: Table S6).
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Justyna Jupowicz-Kozak
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