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. 2011 May 26;6(5):e20199. doi: 10.1371/journal.pone.0020199

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Sudhir et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) The levels of regulated phosphoprotein signatures obtained from quantitative proteomics analysis were subjected to pathway activity analysis. Equations for summarizing the levels of phosphorylated proteins and for analyzing pathway activity are shown. x_i,j and ρ_i,j are the mean and standard deviation, respectively, of the value of the phosphoprotein j in class i, and k is the number of proteins in a given pathway. a_p is the activity score for pathway p between classes c₁ and c₂, and and are the numbers of replicate experiments for the respective classes. In our case, and are each 3. (B) Inferred activities of MAPK and Aurora B signaling pathways in Ras-transformed HBECs and NSCLC cells in comparison with HBEC-3KT are shown as relative pathway activity scores (t-scores). (C) The involvement of the Ras/Raf/MEK/MAPK signaling pathway and its cross-talk with basophilic kinases in NSCLC cells. Kinases identified as being upstream of the regulated phosphosites by NetworKIN analysis in this study are highlighted in bold font. Kinases targeting proline-directed and basophilic S/T sites are labeled in green and blue letters, respectively. The frequencies of the individual kinases identified in A549, H322, and H1299 cells in comparison with HBEC-3KT are shown in parentheses.

Inline graphic — (A) The levels of regulated phosphoprotein signatures obtained from quantitative proteomics analysis were subjected to pathway activity analysis. Equations for summarizing the levels of phosphorylated proteins and for analyzing pathway activity are shown. x_i,j and ρ_i,j are the mean and standard deviation, respectively, of the value of the phosphoprotein j in class i, and k is the number of proteins in a given pathway. a_p is the activity score for pathway p between classes c₁ and c₂, and and are the numbers of replicate experiments for the respective classes. In our case, and are each 3. (B) Inferred activities of MAPK and Aurora B signaling pathways in Ras-transformed HBECs and NSCLC cells in comparison with HBEC-3KT are shown as relative pathway activity scores (t-scores). (C) The involvement of the Ras/Raf/MEK/MAPK signaling pathway and its cross-talk with basophilic kinases in NSCLC cells. Kinases identified as being upstream of the regulated phosphosites by NetworKIN analysis in this study are highlighted in bold font. Kinases targeting proline-directed and basophilic S/T sites are labeled in green and blue letters, respectively. The frequencies of the individual kinases identified in A549, H322, and H1299 cells in comparison with HBEC-3KT are shown in parentheses.