thyroid cancer is one of the most common types of endocrine malignancy , the incidence rate of which has rapidly increased during previous years ( 1,2 ) . it has been estimated that the annual number of cases of thyroid cancer diagnosed in the usa and the associated mortality rate are 12.9/100,000 and 0.5/100,000 individuals , respectively ( 3 ) . papillary thyroid cancer ( ptc ) , characterized by papillary architecture , psammoma bodies and specific nuclear features , including nuclear orientation , nuclear chromatin and nuclear grooving , is the major form of thyroid cancer , accounting for 8085% of all thyroid malignancies ( 4 ) . although ptc has a favorable prognosis , certain cases exhibit aggressive clinical characteristics , including invasion and metastasis , and the management of ptc remains controversial ( 5,6 ) . therefore , it is essential to investigate the molecular mechanisms of ptc and identify potential biomarkers , which may be beneficial for improving treatment . the current understanding of the molecular mechanisms of ptc has improved significantly , particularly with the development of next generation sequencing and microarray technology . it has been reported that mutations of braf ( t1796a and v599e ) causing the activation of serine / threonine kinase may be an alternative mechanism of oncogenic mitogen - activated protein kinase pathway activation and are important in the development of ptc ( 79 ) . the chemokine receptor , cxcr7 not only activates the phosphoinositide 3-kinase / akt and nuclear factor-b signaling pathways , but it also downregulates the notch signaling pathway to regulate the growth and metastasis of ptc , according to gene expression profiling analysis of ptc ( 10 ) . amyloid precursor protein is overexpressed in ptc and may become a potential novel therapeutic target for ptc ( 11 ) . it has been revealed that certain important upregulated micrornas ( mirs ) , including mir-221 , mir-222 and mir-146 , and the regulation of kit are involved in the pathogenesis of ptc , based on previous microarray analysis of gse3467 ( 12 ) . zhu et al ( 13 ) showed that trefoil factor 3 , cut - like homeobox 2 and forkhead box protein a2 are associated with the development of ptc , and the differentially expressed genes ( degs ) are primarily associated with positive regulation of gene expression , gene transcription and metabolic processes . in the previous study by zhu et al ( 13 ) only the gse3678 dna microarray data set was downloaded for deg screening and subsequent enrichment analysis . in the present study , two dna microarray data sets , gse3467 and gse3678 , the degs found to be simultaneously differentially expressed in the tumor samples of these two data sets were screened for enrichment analysis and interaction network construction . gene expression profiles . the two gene expression profiling data sets , gse3467 and gse3678 , were downloaded from the gene expression omnibus ( geo ; http://www.ncbi.nlm.nih.gov/geo/ ) ( 14 ) . gse3467 ( 12 ) consisted of 18 paired tumor and normal thyroid tissue samples from nine patients with ptc . the gse3678 data set contained seven ptc samples and seven paired normal thyroid tissue samples . the platform used for these two data sets was the gpl570 [ hg - u133_plus_2 ] affymetrix human genome u133 plus 2.0 array . the probes without annotation of the gene expression profiles were filtered , and the probes were transformed into gene symbols . the average value of a gene symbol corresponding to multiple probes was calculated for the expression level analysis . the log2 transformation , background correction and data normalization were performed using the genechip robust multi - array analysis ( gcrma ) method within bioconductor ( http://www.bioconductor.org ) ( 15 ) . the degs were screened out by using the linear models for microarray analysis ( limma ) package in r software ( 16 ) with the cut - off criteria of adjusted p<0.01 and |log2 fold - change ( fc)|>2 . functional and pathway enrichment analyses . functional and pathway enrichment analyses for the common degs were performed using the database for annotation , visualization and integrated discovery online tools ( 17 ) based on the gene ontology ( go ) ( 18 ) and kyoto encyclopedia of genes and genomes ( 19 ) databases . the go terms in three categories , including biological process , cellular component and molecular function , were identified with p<0.05 . for pathway enrichment analysis , p0.05 was set as the threshold . construction and analysis of the protein - protein interaction ( ppi ) network . the physical ppis and pathway interactions were selected for ppi network construction using the gene multiple association network integration algorithm ( http://www.genemania.org/ ) ( 20 ) plug - in of cytoscape software ( www.cytoscape.org ; version 3.4.0 ) . the representative subnetwork containing nodes with high levels of interconnection was further derived from the ppi network using molecular complex detection software ( baderlab.org/software/mcode ) ( 21 ) . in addition , the potential drugs of the hub degs in the subnetwork were searched using the drugbank database ( www.drugbank.ca ) ( 22 ) and the potential drug - like ligands , which interacted with the genes , were screened from the diverse - lib database in mtiopenscreen ( bioserv.rpbs.univ-paris-diderot.fr/services/mtiopenscreen ) ( 23 ) according to lipinski 's rule of five ( 24 ) . identification of degs . following data preprocessing , the standardized expression profiling data showed that the median values of gene expression were almost at the same level , indicating that the degree of standardization was sufficient to be used for the subsequent analysis ( fig . a total of 384 and 262 degs were identified for gse3467 and gse3678 , respectively . in addition , 167 genes were found to be simultaneously differentially expressed in the tumor samples of these two data sets ( fig . among these 167 common degs , 77 genes were upregulated and 90 genes were downregulated . the correlation of the expression values for the 167 genes was 0.97 ( p<2.2e-16 ; fig . the common degs were primarily associated with the cellular components of the plasma membrane ( p=2.60e-05 ) and integral to the membrane ( p=0.002429 ) . certain common degs , including lc26a4 , gabrb3 , gabrb2 and clcnkb , were significantly enriched in the anion transmembrane transporter activity ( p=4.45e-04 ) and chloride anion binding ( p=0.005756 ) . in addition , serpina1 , cited1 and ghr were involved with response to steroid hormone stimulus ( p=0.001849 ) . fn1 , lamb3 and col13a1 were enriched in cell adhesion ( p=0.011121 ; table i ) . in addition , two significant pathways were enriched for the common degs ( table ii ) . the aldh1a3 , aox1 , hgd , adh1b and tpo genes were significantly involved in the tyrosine metabolism pathway ( p=0.001 ) . another five common degs , including nrcam , ncam1 , cldn1 , cldn10 and cdh3 , were enriched in the cell adhesion molecules pathway ( p=0.05 ) . interaction network analysis . there were eight common degs , of which met , serpina1 , lgals3 , fn1 , lamb3 , krt19 and col13a1 were upregulated , and tnfrsf11b was downregulated ) in the constructed subnetwork ( fig . 3 ) . the fn1 deg can interact with serpina1 , lgals3 , tnfrsf11b and lamb3 . there were also pathway interactions between any two of the fn1 , col13a1 and lamb3 degs . the potential drugs for fn1 and serpina1 were examined further , as these two degs showed higher degrees in the interaction subnetwork and may be critical in the regulatory process . the results revealed that two drugs , lanoteplase and ocriplasmin , were found for fn1 , and four potential drugs , -mercaptoethanol , recombinant  1-antitrypsin , ppl-100 and api , were found for serpina1 ( table iii ) . lanoteplase is currently under clinical investigation and ocriplasmin , whose pharmacological action involves the cleavage of fibronectin protein , has been approved by the food and drug administration ( 25 ) . for serpina1 , -mercaptoethanol is during experimental stage and the other three drugs are under clinical investigation . in addition , five potential drug - like compounds with binding energies below 8.4 were screened out from the diverse - lib database in mtiopenscreen ( table iv ) . the 24350490 compound , with a binding energy of 8.7 kcal / mol , has six hydrogen bond acceptors and one hydrogen bond donor . another compound , 17506143 , with a binding energy of 8.6 kcal / mol has seven hydrogen bond acceptors and one hydrogen bond donor . the structural interactions between serpina1 and these two drug - like compounds in the present study , 167 genes were identified to be simultaneously differentially expressed in the tumor samples of gse3467 and gse3678 . the subsequent pathway enrichment analysis revealed that aldh1a3 , aox1 , hgd , adh1b and tpo were significantly involved in tyrosine metabolism . several studies have revealed that the protooncogene , ret , which encodes a tyrosine kinase cell surface receptor , is involved in the oncogenesis of ptc by activating its tyrosine kinase , either by rearrangement or mutation ( 26,27 ) . it has been confirmed that the mrna expression level of tpo is markedly suppressed leading to low thyroid peroxidase activity in ptc ( 28 ) . thyroid peroxidase oxidizes iodide to form active iodine for addition onto tyrosine residues on thyroglobulin for the production of thyroid hormones ( 29 ) . in the present study , tpo therefore , aldh1a3 , aox1 , hgd , adh1b and tpo may be important in ptc via their involvement in the tyrosine metabolism pathway . by contrast , the nrcam , ncam1 , cldn1 , cldn10 and cdh3 were significantly enriched in the pathway of cell adhesion molecules . molecules associated with cell adhesion , for example icam-1 , are known to be involved in papillary growth and proliferative capacity ( 30 ) . the pathway enrichment analysis indicated that these common degs are involved in the pathogenesis and progression of ptc by regulating the pathways of tyrosine metabolism and cell adhesion molecules . the representative subnetwork derived from the interaction network in the present study contained seven upregulated common degs ( met , serpina1 , lgals3 , fn1 , lamb3 and col13a1 ) and one downregulated deg ( tnfrsf11b ) . the met , serpina1 , lgals3 and fn1 degs have been identified to be the potent biomarkers for ptc in previous studies ( 31,32 ) . the expression levels of fn1 and met have been also reported to be upregulated in papillary thyroid carcinoma ( 33 ) . the functional enrichment analysis revealed that fn1 was significantly enriched in the plasma membrane , extracellular matrix and cell adhesion . vasko et al ( 34 ) showed that epithelial - to - mesenchymal transition is common in ptc invasion . it has been demonstrated that the genes differentially expressed in aggressive ptc are primarily associated with cell adhesion ( 35 ) . in addition , fn1 can interact with serpina1 , lgals3 , tnfrsf11b and lamb3 , according to the subnetwork . these results suggested that fn1 might be involved in pct by regulating the epithelial - to - mesenchymal transition and interacting with other degs . therefore , ocriplasmin may be of assistance in the prevention or treatment of ptc due to the cleavage of fibronectin . another common deg with a higher degree , serpina1 , was significantly associated with the functions of response to steroid hormone stimulus and response to estrogen stimulus in the present study . vierlinger et al ( 37 ) showed that serpina1 can be considered as a single marker for ptc . in papillary thyroid tumors and normal thyroid tissue , estrogen and progesterone receptors have been identified in thyroid tissue responsive to steroid hormones ( 38 ) . kawabata et al ( 39 ) reported estrogen receptor  ( er ) is expressed at high levels in papillary thyroid cancer , suggesting that er may be involved in the development , physiology and pathology of papillary carcinoma . therefore , upregulated expression levels of serpina1 may contribute to the response to steroid hormones in ptc . in the present study , ser47 are critical for the binding of compounds by forming hydrogen bonds ( 40 ) , the amino acid around the pocket , which binds with compounds , may be critical for the function of serpina1 . therefore , -mercaptoethanol and recombinant  1-antitrypsin may be the potential drugs for ptc . in addition , the gene and protein expression levels of important degs may be better confirmed using experimental studies . in conclusion , the common degs identified from gse3467 and gse3678 were found to have the potential for use as candidate biomarkers for ptc . the upregulated expression levels of fn1 and serpina1 may be involved in ptc by regulating the epithelial - to - mesenchymal transition and response to steroid hormones , respectively . furthermore , ocriplasmin , -mercaptoethanol and recombinant  1-antitrypsin may be potential drugs for the treatment of ptc . in further investigations , confirmation of the expression levels of important genes is required , as is the examination of ptc at different stages .
the present study aimed to systematically examine the molecular mechanisms of papillary thyroid cancer ( ptc ) , and identify potential biomarkers and drugs for the treatment of ptc . 
 two microarray data sets ( gse3467 and gse3678 ) , containing 16 ptc samples and 16 paired normal samples , were downloaded from the gene expression omnibus database . the differentially expressed genes ( degs ) 
 were identified using the linear models for microarray analysis package . 
 subsequently , the common degs were screened for functional and pathway enrichment analysis using the database for annotation visualization and integrated discovery . 
 the representative interaction subnetwork was further derived using molecular complex detection software . 
 in addition , the potential drugs for the hub degs in the subnetwork were screened from drugbank and the potential drug - like ligands , which interacted with genes , were selected using mtiopenscreen . 
 a total of 167 common degs , including 77 upregulated and 90 downregulated degs , were screened . 
 the common degs were associated with the functions of plasma membrane , extracellular matrix , response to steroid hormone stimulus and cell adhesion , and the pathways of tyrosine metabolism and cell adhesion molecules were significantly enriched . 
 a total of eight common degs ( met , serpina1 , lgals3 , fn1 , tnfrsf11b , lamb3 and col13a1 ) were involved in the subnetwork . 
 the two drugs , lanoteplase and ocriplasmin , and four drugs , -mercaptoethanol , recombinant  1-antitrypsin , ppl-100 and api , were found for fn1 and serpina1 , respectively . 
 the common degs identified may be potential biomarkers for pct . 
 fn1 and serpina1 may be involved in ptc by regulating epithelial - to - mesenchymal transition and responding to steroid hormone stimuli , respectively . 
 ocriplasmin , -mercaptoethanol and recombinant  1-antitrypsin may be potential drugs for the treatment of ptc .