Design: Results from the Features-Resource Trade-Off Game were used to form utility weights by ranking functional activities by the relative value of achieving independence in each activity compared with all other component activities.
A list of top ranking functional terms with corresponding statistical parameters are given in Table 2a, 3a, and 4a which correspond to early upregulated genes, early downregulated genes, and early down/late upregulated genes respectively.
The highest ranking functional category identified using IPA was inflammatory response and the highest ranking subcategory within this category- affects immune response-revealed a marked bias in the number of genes displaying a decrease in relative expression (64.5%) compared to those showing an increase in relative expression (35.5%) in PBL from the BTB group.
There are two top ranked functional terms from GSEA annotations (the No. 1 and No. 2 ranked terms) that are directly related to testis-related gene expression as obviously described by the terms themselves (Table 6).
We showed that a recently proposed machine-learning algorithm AODE is well suited to detect and rank functional protein associations being particularly valuable for scenarios characterized by a large proportion of missing values.
Alternatively, enrichment-based analysis [4], [20] [22] can be applied to such a gene list to generate ranked functional categories (e.g., GO) or pathways based on their enrichment levels, so that the significantly enriched pathways and their associated genes can be easily identified as the primary biological themes.
We mapped and ranked functional REs near TSS for all annotated transcripts in UCSC (Additional file 2).
The top ranked functional categories include transcription, regulation of nucleotide metabolism, cell surface receptor-linked signal transduction, protein metabolism, cell organization and biogenesis, cell proliferation, intracellular signaling cascade, defense response and transport.
Despite the presence of highly ranked functional categories (according to Ingenuity p value and number of member miRNAs) that are not readily interpretable in the context of the kidney (e.g. cervical carcinoma, nonobstructive azoospermia), several trends that relate to kidney physiology were evident in the results and are discussed below.
Interestingly, the first ranked functional clusters of five miRNAs (mir-64, mir-248, mir-356, mir-784, and mir-787) are enriched for GO terms related to gonad development, although enrichment is significant only for mir-248, mir-356, and mir-787 after correction for multiple testing (supplementary table S5, Supplementary Material online).
The low-rank functional identification described in Sect.
