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Specific 3-node patterns are found to be functionally enriched in different exogenous cellular conditions and thus may represent significant functional components.
The number of specific enriched words from functional terms (e.g. *auxin*, *photo*, *stress*, *ribosome*; * = wildcard) found to be functionally enriched in LCMs were counted in both keyword and non-keyword groups.
The 95 genes induced at least twofold by toe3 + overexpression were subjected to the Princeton GO Term Finder and found to be functionally enriched in arginine catabolic process (P = 2.4 e-5).
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Global analysis revealed that genes causing reduced fitness when overexpressed resulted mostly in gain-of-function phenotypes and were functionally enriched in transcription factor genes (Gelperin et al. 2005; Sopko et al. 2006; Yoshikawa et al. 2011).
Our results demonstrate that HI genes are functionally enriched in cell-to-cell communication which is a key function for multicellular organisms.
Gene ontology clustering shows that S-nitrosation targets in the LPS/IFN-γ induced RAW264.7 cell model were functionally enriched in protein translation and glycolysis, suggesting that S-nitrosation may function by regulating multiple pathways.
Plenty of DEGs between CYC2 KO and wild type strains were functionally enriched in DNA mismatch repair and DNA replication field, revealing that cyc2p, a cell cycle related protein, would be essential to meiosis by participating in DSBs formations, DNA mismatch repair and replication.
Consistent with this, as expected the target genes shared commonly among multiple tissues in each species are functionally enriched in cell cycle, DNA repair, and DNA replication.
Genes of cluster 7 were functionally enriched in transport.
We found that HI genes were prone to be located in the extracellular part and were functionally enriched in cell-to-cell communication.
The putative target genes of Toe3 were functionally enriched in arginine catabolism, including five that are likely to play a direct role in influencing polyamine levels.
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