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  • genes
  • This method may be used to classify samples based on multi-gene expression patterns and to identify pathways associated with phenotype, without relying upon the differential expression of individual genes. (biomedcentral.com)
  • By applying the PDM on a pathway-by-pathway basis and identifying those pathways that permit unsupervised clustering of samples that match known sample characteristics, we show how the PDM may be used to find sets of mechanistically-related genes that may play a role in disease. (biomedcentral.com)
  • approaches
  • Our results demonstrate that the PDM is able to distinguish cell types and treatments with higher accuracy than is obtained through other approaches, and that the Pathway-PDM application is a valuable technique for identifying disease-associated pathways. (biomedcentral.com)
  • metabolic
  • Here we challenged the validity of this assertion and verified that a transversal metabolic signature in cancer emerges chiefly in the regulation of nucleotide metabolism. (pnas.org)
  • Several common oncogenic pathways have been implicated in the emergence of renowned metabolic features in cancer, which in turn are deemed essential for cancer proliferation and survival. (pnas.org)
  • We observed a metabolic shift that associates differential regulation of enzymes in one-carbon metabolism with high tumor stage and poor clinical outcome. (pnas.org)
  • A significant yet limited set of metabolic genes that explained the partial divergence of ccRCC metabolism correlated with loss of von Hippel-Lindau tumor suppressor ( VHL ) and a potential activation of signal transducer and activator of transcription 1. (pnas.org)
  • Indeed, many common oncogenic signaling pathways have been implicated in the emergence of specific metabolic features in cancer cells that have been associated with both survival and sustained abnormal proliferation rate ( 2 ⇓ ⇓ - 5 ). (pnas.org)
  • Whether due to changes in regulatory tumor suppressors/oncogenes or by acting as metabolic oncogenes themselves, enzymes involved in the complex network of metabolic pathways are being studied to understand their role and assess their utility as therapeutic targets. (hindawi.com)
  • The observed selection toward reduced pyruvate kinase activity may further enable upstream glycolytic intermediates (e.g., 3-phosphoglycerate) to be diverted into other metabolic pathways used to produce the additional lipids, nucleic acids, and proteins that Mullarky et al. (hindawi.com)
  • Figure 6: Proposed mechanism for CDK4/6 inhibitor-mediated manipulation of metabolic pathways. (epgonline.org)
  • In vitro experiments have shown CDK4/6 inhibitors, often in combination with other therapies, are capable of manipulating metabolic pathways and driving cells towards apoptosis or senescence. (epgonline.org)
  • For example, since most of the metabolic reactions dealing with carbon and energy metabolism occur within the cytoplasm, the periplasmic reactions as well as transport reactions between the environment, periplasm and cytoplasm were discarded. (springer.com)
  • Amino acid synthesis is the set of biochemical processes ( metabolic pathways ) by which the various amino acids are produced from other compounds . (thefullwiki.org)
  • In spite of their common hypersaline environment, halophilic archaea are surprisingly different in their nutritional demands and metabolic pathways. (springer.com)
  • The absence of enzyme genes for numerous metabolic reactions in archaeal genomes has limited reconstruction of metabolic pathways so far. (springer.com)
  • tyrosine
  • The novel human proteins (NHPs) described for the first time herein share structural similarity with animal kinases, including, but not limited to, receptor tyrosine kinases (SEQ ID NOS:1-2 show particular similarity to NEK family kinases, and SEQ ID NOS:3-5 are particularly similar to calcium and calmodulin dependent kinases as well as sequences encoding PK 80), and serine-threonine kinases. (google.de)
  • betaine
  • Cho has multiple roles in metabolism including incorporation into membrane phospholipids such as phosphatidylcholine (PC) and sphingomyelin, neurotransmitter formation (i.e., acetylcholine), and mitochondrial oxidation to betaine (Bet), a critical osmolyte and methyl-group donor in one carbon metabolism. (frontiersin.org)
  • Glycolysis
  • Exemplified by cancer cells' preference for glycolysis, for example, the Warburg effect, altered metabolism in tumorigenesis has emerged as an important aspect of cancer in the past 10-20 years. (hindawi.com)
  • carbon
  • Further network-dependent analyses revealed unique defects in nucleotide, one-carbon, and glycerophospholipid metabolism at the transcript and protein level, which contrasts findings in other tumors. (pnas.org)
  • The carbon backbones come from the glycolytic pathway , the pentose phosphate pathway , or the citric acid cycle . (thefullwiki.org)
  • In each of the 19 pathways for the generation of chiral amino acids, the stereochemistry at the α-carbon atom is established by a transamination reaction that involves pyridoxal phosphate. (thefullwiki.org)
  • Tetrahydrofolate , a carrier of activated one-carbon units, plays an important role in the metabolism of amino acids and nucleotides. (thefullwiki.org)
  • dehydratase
  • Yamada T, Komoto J, Kasuya T, Takata Y, Ogawa H, Mori H, Takusagawa F: A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: crystal structure and site-directed mutagenesis studies. (hmdb.ca)
  • Serine dehydratase and threonine dehydratase. (cram.com)
  • Protein
  • Although haloarchaea share certain features in order to adapt to their extreme environment, i.e. acidic protein machineries, respiratory chains and rhodopsins, their metabolism is considerably different from each other. (springer.com)
  • genomes
  • A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. (beds.ac.uk)
  • processes
  • Peroxisome proliferator-activated receptor gamma (PPARγ) is a member of the nuclear receptor superfamily of ligand-activated transcription factors [ 10 ] and has been shown to be involved in many diverse biological processes, including adipogenesis and glucose and lipid metabolism. (biomedcentral.com)
  • The most relevant biochemical processes related to folic acid in the context of metabolism, oxidation and inflammation are represented. (wikipathways.org)
  • whereas
  • This is consistent with the previous observation that Toxoplasma can synthesise serine, whereas Plasmodium has an auxotrophic requirement for serine from hosts [ 1 ]. (llamp.net)
  • 27 ] found that both the Calvin-Benson-Bassham cycle and the Wood-Ljungdahl pathway occurred most frequently, whereas the TCA cycle was little used in Woesearchaeota. (beds.ac.uk)
  • regulation
  • It is suggested that regulation of metabolism is a point of convergence of many different cancer-associated pathways. (pnas.org)
  • Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis. (northwestern.edu)
  • Over the past 10-20 years, increasing evidence has shown that the majority of oncogenes and tumor suppressors also play a role in the regulation of metabolism. (hindawi.com)
  • cancers
  • However, the extent to which different cancers coordinate their metabolism to meet these requirements is largely unexplored. (pnas.org)
  • The importance of serine metabolism in multiple cancers is increasingly apparent, and how the metabolism of this amino acid influences cancer phenotypes is an area of active investigation. (rupress.org)
  • cancer phenotypes
  • There is now widespread consensus that diversion of metabolism is among the most distinguished cancer phenotypes, and it is often postulated to characterize virtually all forms of cancer ( 1 , 2 ). (pnas.org)
  • sequences
  • As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown. (beds.ac.uk)
  • moreover
  • Methyl groups are of vital importance in the metabolism of all animals, moreover, animals cannot synthesize methyl groups and thus need to receive them in their diets. (allaboutfeed.net)
  • Moreover we have also identified new pathways induced in ob/ob islets that remained unchanged in POKO islets, suggesting an important role for PPARγ in maintenance/activation of mechanisms essential for the continued function of the beta cell. (biomedcentral.com)