Differential miRNA expression profiling of highly pathogenic avian influenza virus H5N1 infected chicken lungs reveals critical microRNAs, biological pathways and genes involved in the molecular pathogenesis

• Highthrouput sequencing of small RNA of H5N1 infected and mock infected chicken lungs. • 297 miRNAs identified in mock-infected and 201 miRNAs identified in AIV infected chicken lungs. • 36 miRNAs were upregulated and 90 were downregulated during H5N1 infection. • Functional analysis and gene ontology of predicted target genes of expressed miRNAs. • MAPK pathway, NF-κB, IGF and gga-let-7b might play important role during H5N1 pathogenesis.