title: Identification of differential pathways in papillary thyroid carcinoma utilizing pathway co-expression analysis.
abstract: OBJECTIVE
  To identify differential pathways between papillary thyroid carcinoma (PTC) patients and normal controls utilizing a novel method which combined pathway with co-expression network.
  
  
  METHODS
  The proposed method included three steps. In the first step, we conducted pretreatments for background pathways and gained representative pathways in PTC. Subsequently, a co-expression network for representative pathways was constructed using empirical Bayes (EB) approach to assign a weight value for each pathway. Finally, random model was extracted to set the thresholds of identifying differential pathways.
  
  
  RESULTS
  We obtained 1267 representative pathways and their weight values based on the co-expressed pathway network, and then by meeting the criterion (Weight > 0.0296), 87 differential pathways in total across PTC patients and normal controls were identified. The top three ranked differential pathways were CREB phosphorylation, attachment of GPI anchor to urokinase plasminogen activator receptor (uPAR) and loss of function of SMAD2/3 in cancer.
  
  
  CONCLUSIONS
  In conclusion, we successfully identified differential pathways (such as CREB phosphorylation, attachment of GPI anchor to uPAR and post-translational modification: synthesis of GPI-anchored proteins) for PTC using the proposed pathway co-expression method, and these pathways might be potential biomarkers for target therapy and detection of PTC.
authors.affiliation: Department of Endocrinology, Binzhou People's Hospital, Binzhou, 256600, Shandong Province, China.
authors.forename: Wei-Hai
authors.initials: WH
authors.lastname: Qiu
authors.forename: Gui-Yan
authors.initials: GY
authors.lastname: Chen
authors.forename: Lu
authors.initials: L
authors.lastname: Cui
authors.forename: Ting-Ming
authors.initials: TM
authors.lastname: Zhang
authors.forename: Feng
authors.initials: F
authors.lastname: Wei
authors.forename: Yong
authors.initials: Y
authors.lastname: Yang
mesh_terms: D001499:Bayes Theorem; D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism; D002277:Carcinoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D002291:Carcinoma, Papillary; D016022:Case-Control Studies; D019295:Computational Biology; D017362:Cyclic AMP Response Element-Binding Protein / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D005240:Feasibility Studies; D058851:GPI-Linked Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D010766:Phosphorylation; D055293:Receptors, Urokinase Plasminogen Activator / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D051899:Smad2 Protein / Q000235:genetics / Q000378:metabolism; D051900:Smad3 Protein / Q000235:genetics / Q000378:metabolism; D000077273:Thyroid Cancer, Papillary; D013964:Thyroid Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor; C115163:CREB1 protein, human; D017362:Cyclic AMP Response Element-Binding Protein; D058851:GPI-Linked Proteins; C524898:PLAUR protein, human; D055293:Receptors, Urokinase Plasminogen Activator; C497782:SMAD2 protein, human; C497790:SMAD3 protein, human; D051899:Smad2 Protein; D051900:Smad3 Protein