spinal cord injury harms the physical and mental condition of patients and causes substantial economic burden to society . therefore , the prevention and treatment of spinal cord injury has become an important topic in medicine . scientists are investigating various avenues for treatment of spinal cord injury ; however , aside from methylprednisolone , none of these developments have reached even limited use in the clinical care of human spinal cord injury patients in the usa . microarray data analysis features high throughput and high sensitivity , which has made it possible to test the expression changes of the whole genome . therefore , the development of microarray analysis has provided new insights into diagnosis and treatment of sci [ 79 ] . toshiya , using complementary dna microarray analysis , identified 3 up - regulated and 7 down - regulated genes that may play a role in response to tissue damage or repair following sci . however , most of these reports only concentrated on several individual genes , lacking overall data . in addition , the degs of interest were rarely the same in different reports , and results of analysis of chips varied due to many factors , such as samples , platforms , and analysis methods . thus , many experts have made great efforts to obtain reliable results from chips by use of meta - analysis ; however , many essential issues , such as annotation and comparison of cross - platforms , could not be solved appropriately . in the present study we identified 113 differentially expressed mirnas between normal and spinal cord injury patients . then we constructed a ppi network by use of the string database to explore 3 function modules to determine the biological processes and signal pathways they were involved in . we found no significant differences in signal pathway between genes participating in function module 1 and all 113 degs . eventually , we found that a critical protein , actc1 , could function as a prognostic and predictive marker in clinical treatment of sci . the microarray expression profiles of spinal cord injury were extracted from the geo ( gene expression omnibus , http://www.ncbi.nlm.nih.gov/geo/ ) database under the accession number of gse33886 . a total of 7 specimens divided into 2 groups were available for the analysis , including 4 samples from normal vastus lateralis leg tissues and 3 specimens from leg tissues of patients with spinal cord injury . the original data are preprocessed by rma function in the affymetrix package   of r language . the original cel files were converted into probe expression measures , and the probe - level data were converted into gene names by an annotation package based on the bioconductor platform . probes matching more than 1 gene were eliminated and the average value was used for probes matching the same single gene . degs that were significantly differentially expressed among the mesenchymal stem cell samples from sci patients and the matched normal tissues were screened out by use of the limma package   in r language . fold change > 2 was used as the threshold to determine the significance of gene expression difference . we used cluster analysis and the corresponding cluster figure to ensure that the screened genes perfectly expressed the differences between samples of sci patients and the matched normal tissues . the david ( database for annotation visualization and integrated discovery ) database   was used to perform the go functional and kegg pathway analysis . significantly enriched go terms and kegg pathways with fdr ( fold discovery rate ) < 0.05 were screened out . protein - protein interactions regulating differentially expressed genes were obtained by use of string ( http://string-db.org/ ) , a database of known and predicted protein - protein interactions . topology characters of the ppi network , such as network nodes contribution , the shortest path , the average assemble coefficient , and centrality , were analyzed by use of network analyzer   in cytoscape software . then , the regulation relationship of each gene was obtained and kegg pathway enrichment analysis was performed on the nodes in the network . p - value less than 0.05 and nodes larger than 5 were used as the cut - off criteria . the microarray expression profiles of spinal cord injury were extracted from the geo ( gene expression omnibus , http://www.ncbi.nlm.nih.gov/geo/ ) database under the accession number of gse33886 . a total of 7 specimens divided into 2 groups were available for the analysis , including 4 samples from normal vastus lateralis leg tissues and 3 specimens from leg tissues of patients with spinal cord injury . the original data are preprocessed by rma function in the affymetrix package   of r language . the original cel files were converted into probe expression measures , and the probe - level data were converted into gene names by an annotation package based on the bioconductor platform . probes matching more than 1 gene were eliminated and the average value was used for probes matching the same single gene . degs that were significantly differentially expressed among the mesenchymal stem cell samples from sci patients and the matched normal tissues were screened out by use of the limma package   in r language . fold change > 2 was used as the threshold to determine the significance of gene expression difference . we used cluster analysis and the corresponding cluster figure to ensure that the screened genes perfectly expressed the differences between samples of sci patients and the matched normal tissues . the david ( database for annotation visualization and integrated discovery ) database   was used to perform the go functional and kegg pathway analysis . significantly enriched go terms and kegg pathways with fdr ( fold discovery rate ) < 0.05 were screened out . protein - protein interactions regulating differentially expressed genes were obtained by use of string ( http://string-db.org/ ) , a database of known and predicted protein - protein interactions . interactions with scores higher than 0.4 were screened out to construct the ppi network . topology characters of the ppi network , such as network nodes contribution , the shortest path , the average assemble coefficient , and centrality , were analyzed by use of network analyzer   in cytoscape software . then , the regulation relationship of each gene was obtained and kegg pathway enrichment analysis was performed on the nodes in the network . p - value less than 0.05 and nodes larger than 5 were used as the cut - off criteria . comparison analysis of functional enrichment between selected modules and all the degs was performed . microarray data of 19 433 genes from 7 samples were obtained after data preprocessing . data before and after normalization are listed in figure 1 . a total of 113 degs were identified between 4 normal and 3 spinal cord injury specimens , including 54 up - regulated and 59 down - regulated genes , accounting for 47.78% and 52.22% , respectively , of all the degs ( figure 2 , table 1 ) . there were no significantly enriched go terms or pathways among the up - regulated genes ( table 2 ) . down - regulated genes were enriched in more than 1 go term and kegg pathways . among the up - regulated genes , 21 genes were enriched in 7 biological processes , including fatty acid metabolism , system regulation , and ventricle morphology . we found 16 down - regulated genes enriched in pathways composed by cells , including sarcomere , actin cytoskeleton , and muscle fibril . nine down - regulated genes were significantly enriched in 4 kegg pathways , including myocardial contraction , hypertrophic cardiomyopathy , dilated cardiomyopathy , and ppar signal pathway . a total of 73 protein - protein interaction pairs with reliability scores higher than 0.4 were screened out , each with 40 codes , accounting for 35.39% of all degs . the ppi network of degs appeared to have high cluster properties ( figure 3 ) . three modules were selected out with the threshold of node > 5 and p - value < 0.05 by clusterone plug in cytoscape ( table 3 , figure 5 ) . eight genes were enriched in 29 biological pathways in the first module , while 10 genes were enriched in 18 pathways related with molecule functions . several pathways associated with biological process were enriched , but no obvious signaling pathway or molecular function was enriched in the second or the third module ( table 5 ) . twelve biological processes , 9 cell constitution , 2 molecular function , and 3 kegg pathways were enriched in 3 function modules and all degs ( figure 6 ) , except for 5 biological processes that were enriched in the degs but not in the function module . this result revealed that there was no obvious difference in signaling pathways between the 11 genes that participated in module 1 and the 113 differentially expressed genes . microarray data of 19 433 genes from 7 samples were obtained after data preprocessing . data before and after normalization are listed in figure 1 . a total of 113 degs were identified between 4 normal and 3 spinal cord injury specimens , including 54 up - regulated and 59 down - regulated genes , accounting for 47.78% and 52.22% , respectively , of all the degs ( figure 2 , table 1 ) . there were no significantly enriched go terms or pathways among the up - regulated genes ( table 2 ) . down - regulated genes were enriched in more than 1 go term and kegg pathways . among the up - regulated genes , 21 genes were enriched in 7 biological processes , including fatty acid metabolism , system regulation , and ventricle morphology . we found 16 down - regulated genes enriched in pathways composed by cells , including sarcomere , actin cytoskeleton , and muscle fibril . nine down - regulated genes were significantly enriched in 4 kegg pathways , including myocardial contraction , hypertrophic cardiomyopathy , dilated cardiomyopathy , and ppar signal pathway . a total of 73 protein - protein interaction pairs with reliability scores higher than 0.4 were screened out , each with 40 codes , accounting for 35.39% of all degs . the ppi network of degs appeared to have high cluster properties ( figure 3 ) . three modules were selected out with the threshold of node > 5 and p - value < 0.05 by clusterone plug in cytoscape ( table 3 , figure 5 ) . eight genes were enriched in 29 biological pathways in the first module , while 10 genes were enriched in 18 pathways related with molecule functions . several pathways associated with biological process were enriched , but no obvious signaling pathway or molecular function was enriched in the second or the third module ( table 5 ) . twelve biological processes , 9 cell constitution , 2 molecular function , and 3 kegg pathways were enriched in 3 function modules and all degs ( figure 6 ) , except for 5 biological processes that were enriched in the degs but not in the function module . this result revealed that there was no obvious difference in signaling pathways between the 11 genes that participated in module 1 and the 113 differentially expressed genes . in this study we identified 113 differentially expressed genes from the most significantly altered genes using data from 2 datasets on the same platform of the geo dataset , which can effectively avoid differences resulting from many factors , such as different samples , platforms , and analysis methods . much of the previous research concentrated on the several genes they selected instead of the overall data . although much effort was made , such as using meta - analysis to obtain more reliable results , critical problems could not be solved , such as annotation and comparison of trans - platforms . our study effectually overcomes the above defects by using 2 datasets on the same platform , thus enhancing the reliability of our results . as 2-gene interaction is more sensitive and accurate in clinical prognosis and diagnosis of sci compared to use of a single gene , we selected 40 interacting genes by string method to construct a ppi network for better analysis of data , which turned out to be a network with biological functionality . the ppi network of degs in our study appeared to be highly clustered , which is the essential character of a biological network , reflecting a high degree of modularization . we divided the network into 3 separate modules and performed functional enrichment analysis on these 3 modules . the ppi network we constructed in the research was larger and more reliable than the previous ones . three function modules  cardiac muscle contraction ( hsa05410 ) , hypertrophic cardiomyopathy ( hcm ) ( hsa05414 ) , and dilated cardiomyopathy ( hsa04260 )  were explored using clusterone . actc1  was found to be up - regulated , while myosin heavy - chain 6 ( myh6 ) , myosin heavy - chain 7 ( myh7 ) , and myosin light - chain 3 ( myl3 ) were down - regulated . in addition , the availability and rationality of these functions were supported by the fact that there was no obvious difference between the signal pathway participation of genes in module 1 and those of all the degs , which make our results more reliable . our results suggest a potential application of target genes and the proteins they express as prognostic and predictive markers in development and improvement of sci therapies . stat3 ( signal transducer and activator of transcription 3 ) was reported to be involved in scar formation after spinal cord injury by regulating astrocyte activity , which can in turn restrict the spread of inflammatory cells after sci . in another study , the rho signaling pathway was reported to be a potential target for therapeutic interventions after spinal cord injury . however , these studies concentrated primarily on pathways after spinal cord injury , and there has been little research into the mechanisms that regulate the progression and development of sci . in this study , through comparing functions between module 1 and all the degs , we obtained 3 pathways  the myocardium contraction pathway , hypertrophic cardiomyopathy pathway , and the dilated cardiomyopathy pathway  that may function as predictors of clinical outcome in sci patients . evidence from previous research showed that sci has many common complications , and cardiac dysfunctions were among the most important complications following sci . cardiovascular disturbances were proven to be the leading causes of morbidity and mortality in both acute and chronic stages of sci . therefore , we suggest that the 3 significantly enriched pathways found this study may be associated with the occurrence of spinal cord injury because cardiovascular deconditioning may lead to loss of skeletal muscle pumping activity . actc1 protein , the critical protein in these 3 pathways , was significantly up - regulated , while myosin heavy - chain 6 ( myh6 ) , myosin heavy - chain 7 ( myh7 ) , and myosin light - chain 3 ( myl3 ) were down - regulated . therefore , it is important to study the regulation mechanism of actc1 to help understand its role in predicting targets in the injury process in sci patients . the up - regulation of actc1 can affect the myofilament contraction in the myocardium contraction pathway , and the state of striated muscle in hypertrophic cardiomyopathy pathway and the dilated cardiomyopathy pathway . in fact , in the last decade , actc1   has increasingly been recognized as an important property of muscle state . it mediates a variety of essential biological functions in all eukaryotic cells , providing a structural framework around which cells shape themselves . our results in the present study suggest its momentous role in the cytoskeleton and a potential role as a prognostic factor and predictor in clinical management of sci patients . in addition , we discovered that degs were significantly enriched in cytoskeleton - dependant intracellular transport ( go : 0030705 ) and actin filament - based movement ( go : 0030048 ) , confirming the role of actin in sci development and progression . we also that found myosin heavy - chain 6 ( myh6 ) , myosin heavy - chain 7 ( myh7 ) , and myosin light - chain 3 ( myl3 ) were down - regulated . recent studies have discovered that the regulation of mhc isoform expression involves a complex interaction of multiple control mechanisms , including myogenin and calcineurin , and indicated that other intracellular signaling pathways were also likely to contribute . the enriched pathway in the present study  muscle tissue morphogenesis ( go : 0060415 )  is likely involved in the progression of sci by participating in this process . additionally , it has been reported that mutations in myh6 can cause a spectrum of phenotypes , ranging from hcm ( hypertrophic cardiomyopathy to dcm ( dilated cardiomyopathy ) , which is correlated with the pathways that were found to be enriched in our study  the hypertrophic cardiomyopathy pathway and the dilated cardiomyopathy pathway . thus , we hypothesize that down - regulation of myhc is related with sci and has a potential to function as a new marker in clinical diagnosis and development of therapies for sci . three function modules were explored using clusterone and 3 enriched signaling pathways were found : the myocardium contraction pathway , the hypertrophic cardiomyopathy pathway , and the dilated cardiomyopathy pathway . we found no differences among the signal pathways between genes participating in module 1 and all the degs , confirming its potential role as a prognostic and predictive indicator for use in sci patients . moreover , critical proteins , such as actc , myh6 , myh7 , and myl3 , in the enriched pathways may also provide useful information for better understanding of genetic changes in sci .