Synechococcus elongatus PCC7942 represents a classical microbial model that has been widely studied. Its genome-scale metabolic network was recently published (iSyf715), allowing the integration of high-throughput data with the network connectivity. The high-dimensionality of this analysis paves the way not only for the designing of metabolic engineering strategies but also for the principles elucidation of certain cellular processes functioning. Here we present a reporter metabolites analysis of transcriptional profile of S. elongatus PCC7942 under inorganic carbon acclimation by the integration with the connectivity structure of iSyf715. The analysis is based on the published transcriptional changes after 6 and 24 hours of cells growth, when the CO₂ concentration was shifted from high to low levels. The Reporter Features algorithm was applied to unveil the 52 scattered reporter metabolites (p<0.05) across the whole cyanobacterium metabolism, which could represent key regulatory nodes during the CO₂ regime transitions. In addition, clusters of metabolic genes that significantly and coordinately change their expression during this perturbation were identified by using the Reporter Subnetwork algorithm. These results could support the subsequent inference of feasible transcriptional regulatory maps as well as the assessment of the metabolic network capabilities of iSyf715.