Abstract: Cold stress is one of the major environmental limitations to agricultural productivity throughout the world. Overcoming the defects of microarray sequencing analyses caused by heterogeneity in individual studies and prediction of cold stress response candidate genes and pathways in Arabidopsis thaliana are requisite for cold tolerant crop-plant design and mining potential salt responses mechanisms. A literature searching strategy was used to identify salt stress response expression profiling studies in Arabidopsis from the PubMed database, the Gene Expression Omnibus(GEO) database, and the ArrayExpress database. Eight studies were filtered from the 1 166, 298 and 695 identified studies. The batch effect correction and the effect size analysis based on the NetworkAnalyst web tool were combined to integrate 8 microarray datasets, and 1 553 up-regulated and 4 327 down-regulated were identified with in low temperature treated samples. From the functional enrichment analyses results and the differently spatio-temporal expression patterns of transcriptional factors(TFs), protein kinases(PKs) and several plant hormone-related genes, plant hormone related stress signal construction pathways, ion and protein kinases related signaling pathways and transcriptional regulation were predicted to participate in regulating cold stress response in Arabidopsis.