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We determined Gene Ontology (GO) biological processes for genes that were strong candidates for regulation by Elongator including downregulated proteins encoded by transcripts with an AA AG > 1.3 and size ≥ 1,005 codons, as well as upregulated proteins with an AA AG bias of < 0.3 and transcript size ≤ 300 codons (Fig. 3, Supplementary Data 9).
Networks, canonical pathways and functional processes for genes passing either the FDR p < 0.05 and an absolute fold change of two or more criteria and/or SigPathway filter FDR p < 0.05 were analysed using IPA.
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With this emergent behavior, the role of MyD88, TRIF and novel MyD88, TRIF-independent processes for gene induction can be linearly superposed to decipher quantitative whole genome differential control of transcriptional and mRNA decay machineries.
Nucleosome remodeling and histone deacetylation are the major processes for gene transcriptional regulation [ 10].
Intrinsic noise arises from the inherent randomness during transcription and translation, key processes for gene expression [ 4].
In addition, Pathway Studio was used to determine over-represented physiological processes for gene lists based on KEGG, PANTHER (Protein ANalysis THrough Evolutionary Relationships) and NCBI GO (National Center for Biotechnology Information Gene Ontology) databases.
The predominant biological process for genes from the arctic-enriched library is "response to stimulus".
We undertook a careful confirmation process for genes targeted by the top 20 scoring siRNAs.
The RNA samples were further processed for genes expression analysis by microarray and small RNA analysis by deep sequencing.
Locus, description, log fold change (logFC), and gene ontology terms (biological process) for genes found specifically up- and down-regulated in P. cheesemanii, P. exile and P. novae-zelandiae when compared to the two remaining species combined.
However, the tissues were not processed for gene expression studies to determine what bone formation pathways might contribute to these structural adaptations.
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