For example, the GO restricts usage of evidence based on expression pattern to annotations with terms from the biological process ontology.
For such cases, protein network data provide an additional piece of evidence for the correct functional assignment based on expression clustering (Table S2).
Similar to MBA, mCADRE emphasizes the inclusion of a high-confidence core set of reactions from a generic genome-scale model, based on tissue-specific expression evidence.
An additional 304 regions (custom ranges) not annotated as coding sequences are also represented on the array based on evidence for expression from tiling array data generated in conjunction with the genome project (Richards et al. 2008).
Based on limited evidence of gene expression data from four studies involving 43 patients, the following remarks can be made: 1.
However, as this association is based on indirect evidence from heterologous expression and computational modeling experiments, more studies examining the relationship between the relative abundance of ERG1 isoforms and restitution kinetics in cardiac tissue are needed to determine if this predicted association is also evident in vivo.
Candidate genes (shown in Supplementary Table S1) were selected for gene expression analysis, based on previous evidence that they may be linked to the sensitivity or resistance to EGFR-inhibitor drugs either directly (as components of the EGFR signaling pathway) or indirectly (by marking fundamental pathobiological variables such as cell cycle activity, or stromal response).
While a core set of high-confidence reactions in MBA is determined based on gene expression or literature evidence, the ranking and inclusion of non-core reactions is based on iterative model simulation for many different random reaction orderings.
The maternal transcription factor Sall4 binds to the Oct4 DE, and it is regarded to be a transcriptional activator of Oct4 expression based on evidence that reduction in Sall4 mRNA level in blastocysts at merely 50% knockdown efficiency by Sall4 siRNA injection into zygotes led to a 70% reduction in Oct4 expression [ 68].
Albeit preliminarily, this test shows correspondence between the number of ESTs for a given gene and the qPCR estimation of gene expression, but conclusions based on this evidence must be taken with caution until a more rigorous experiment is conducted.
