ProteoMirExpress: inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data.
MicroRNAs (miRNAs) regulate gene expression through translational repression and RNA degradation. Recently developed high-throughput proteomic methods measure gene expression changes at protein level and therefore can reveal the direct effects of miRNAs' translational repression. Here, we present a web server, ProteoMirExpress, that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks. With both types of high-throughput data from the users, ProteoMirExpress is able to discover not only miRNA targets that have decreased mRNA, but also subgroups of targets with suppressed proteins whose mRNAs are not significantly changed or with decreased mRNA whose proteins are not significantly changed, which are usually ignored by most current methods. Furthermore, both direct and indirect targets of miRNAs can be detected. Therefore, ProteoMirExpress provides more comprehensive miRNA-centered regulatory networks. We used several published data to assess the quality of our inferred networks and prove the value of our server. ProteoMirExpress is available online, with free access to academic users.
Department of Biochemistry, The University of Hong Kong, Hong Kong SAR, China;
Jing
J
Qin
Mulin Jun
MJ
Li
Panwen
P
Wang
Nai Sum
NS
Wong
Maria P
MP
Wong
Zhengyuan
Z
Xia
George S W
GS
Tsao
Michael Q
MQ
Zhang
Junwen
J
Wang
D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D053263:Gene Regulatory Networks; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000706:statistics & numerical data; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D020543:Proteome / Q000235:genetics* / Q000378:metabolism*; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*; D012984:Software
D035683:MicroRNAs; D020543:Proteome; D012333:RNA, Messenger