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The 1687 genes regulated by SRA overexpression, the 340 genes regulated by SRA knockdown, and the 60 intersection genes were each analyzed for over-representation of Gene Ontology (GO) biological processes (BP) and molecular functions (MF).
As shown in Data Set S3, four intersection genes associated with inflammation were negatively regulated by SRA.
Sixty genes/ESTs (intersection genes) were commonly regulated (and in opposite directions) by SRA overexpression in ST2 adipocytes and endogenous SRA knockdown in 3T3-L1 adipocytes.
We focused our attention primarily on these intersection genes, since they are more likely to be of significance for adipocyte biology.
Therefore it is interesting that the most enriched GO term associated with the intersection genes is Inflammatory Response, and the fourth such GO term is Regulation of Cytokine Biosynthetic Process (Table 5).
These studies resulted in the identification of 1687 genes with altered expression between SRA overexpresing and control ST2 adipocytes, 340 genes that differed in expression between SRA knockdown and control 3T3-L1 andpocytesixtyd sintersectionction genes that were oppositely regulated by SRA overexpression and knockdown.
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Two of the top 5 intersection gene GO-BP terms are Cell Division and M Phase (Table 5).
ChIPseeqer provides functionality of area intersection, gene mapping and finding of known public TFBS motifs.
For each union intersection, gene IDs of the top lists of metastasis data frames were combined into a vector and gene IDs of the top lists of hypoxia data frames were combined into another one.
Permutation analysis yielded a maximum intersection gene list size of 10 genes only 3 times in 100,000 trials inferring a p-value close to zero for the 234 genes found in common to the regional metagenes listed in Additional File 1.
When the proliferation metagenes were derived de novo for each of the individual datasets, by identifying the proliferation cluster as above, the correlation of this de novo proliferation metagene to the proliferation metagene from the intersection gene list was always high (worst case 0.956).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com