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However, with the better acoustic modeling of the text-based DNN STD system, the performance is better than that of the DTW-based systems, which confirms the potential of DNNs in STD, especially when the correct term transcription is employed in the search.
First, the genecentric construction was repeated, but constrained to those genes whose GO [13] annotation contains the term "transcription".
In support of this prediction, the GO term "transcription repressor activity" from the molecular function field is enriched (Figure S1 and Table S3), again suggesting that the light input to clock entrainment may act via transcriptional repressor functions.
Also, among newly recovered genes that have the GO term "transcription from RNA polymerase II promoter" by adding motif information, nine proteins have a protein motif "Zinc finger, C2H2 type, domain".
Twenty proteins in the data set (21%) are annotated with the GO term "transcription factor activity".
Typical in this sense were our results for the child GO term Transcription activator activity.
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Importantly, our study identified a large proportion of differentially expressed genes (97) related to transcriptional regulation, based on the GO terms "transcription regulator activity", "transcription factor activity", and "transcription repressor activity" (Additional file 6).
The Chinnaiyan laboratory extended their seminal TMPRSS2-ERG study by using RNAseq to identify 11 other fusion transcripts that are not produced by chromosomal alterations (hereafter termed transcription-induced transcripts) [ 12, 13].
In silico analysis found similar enrichments in both regions for biologic process terms, transcription factor binding and miRNA target motifs.
The Venn diagram shows the number of these genes associated with GO biological process terms "transcription factor activity" (GO 0003700), "transcription cofactor activity" (GO 0003712) and "DNA binding" (GO 0003677).
We compared this transportation network with two transcriptional regulatory networks, which relate the expression of genes (nodes) that interact by producing proteins, termed transcription factors, that may alter the expression level of other genes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com