User:HassanForoughiAsl/2 July 2010

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(Difference between revisions)
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#[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003911 Prieto et. al. (2008)] Used KEGG for their study of functional interaction, used method: ''"The data used in this work corresponds to a set of human genome-wide expression microarrays hybridized with mRNA samples coming from different human tissues, glands or organs from healthy normal individuals."'' With notes from [https://2010.igem.org/User:HassanForoughiAsl/1_July_2010 yesterday] about this article, I think these information could help us understand which genes and prot. interaction to trust.
#[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003911 Prieto et. al. (2008)] Used KEGG for their study of functional interaction, used method: ''"The data used in this work corresponds to a set of human genome-wide expression microarrays hybridized with mRNA samples coming from different human tissues, glands or organs from healthy normal individuals."'' With notes from [https://2010.igem.org/User:HassanForoughiAsl/1_July_2010 yesterday] about this article, I think these information could help us understand which genes and prot. interaction to trust.
#[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000807 De Las Rivas et al 2010]
#[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000807 De Las Rivas et al 2010]
-
:*''"As discussed previously ([[#Reference] 1], [http://dx.doi.org/10.1016/j.tibs.2008.04.002 Andrew Chatr-aryamontri et al 2008]), the issue of whether two proteins share a “functional contact” is quite distinct from the question of whether the same two proteins interact directly with each other. Any protein in the ribosome or in the basal transcriptional apparatus shares a functional contact with the other proteins in the complex, but certainly not all the proteins in the particular complex interact."''
+
:*''"As discussed previously ([[#Reference|1]], [http://dx.doi.org/10.1016/j.tibs.2008.04.002 Andrew Chatr-aryamontri et al 2008]), the issue of whether two proteins share a “functional contact” is quite distinct from the question of whether the same two proteins interact directly with each other. Any protein in the ribosome or in the basal transcriptional apparatus shares a functional contact with the other proteins in the complex, but certainly not all the proteins in the particular complex interact."''
:*''"Another essential element for defining PPIs is the biological context. Not all possible interactions will occur in any cell at any time. Instead, interactions depend on cell type, cell cycle phase and state, developmental stage, environmental conditions, protein modifications (e.g., phosphorylation), presence of cofactors, and presence of other binding partners."''
:*''"Another essential element for defining PPIs is the biological context. Not all possible interactions will occur in any cell at any time. Instead, interactions depend on cell type, cell cycle phase and state, developmental stage, environmental conditions, protein modifications (e.g., phosphorylation), presence of cofactors, and presence of other binding partners."''
:*''"The techniques that measure direct physical interactions between protein pairs are “binary” methods, while the techniques that measure physical interactions among groups of proteins, without pairwise determination of protein partners, are “co-complex” methods"''
:*''"The techniques that measure direct physical interactions between protein pairs are “binary” methods, while the techniques that measure physical interactions among groups of proteins, without pairwise determination of protein partners, are “co-complex” methods"''

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Continuation from yesterday
  1. [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003911 Prieto et. al. (2008)] Used KEGG for their study of functional interaction, used method: "The data used in this work corresponds to a set of human genome-wide expression microarrays hybridized with mRNA samples coming from different human tissues, glands or organs from healthy normal individuals." With notes from yesterday about this article, I think these information could help us understand which genes and prot. interaction to trust.
  2. [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000807 De Las Rivas et al 2010]
  • "As discussed previously (1, [http://dx.doi.org/10.1016/j.tibs.2008.04.002 Andrew Chatr-aryamontri et al 2008]), the issue of whether two proteins share a “functional contact” is quite distinct from the question of whether the same two proteins interact directly with each other. Any protein in the ribosome or in the basal transcriptional apparatus shares a functional contact with the other proteins in the complex, but certainly not all the proteins in the particular complex interact."
  • "Another essential element for defining PPIs is the biological context. Not all possible interactions will occur in any cell at any time. Instead, interactions depend on cell type, cell cycle phase and state, developmental stage, environmental conditions, protein modifications (e.g., phosphorylation), presence of cofactors, and presence of other binding partners."
  • "The techniques that measure direct physical interactions between protein pairs are “binary” methods, while the techniques that measure physical interactions among groups of proteins, without pairwise determination of protein partners, are “co-complex” methods"


Reference =
  1. [http://dx.doi.org/10.1016/j.tibs.2007.09.006 Joel P. Mackay et al 2007]
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