This study investigates homotopic functional connectivity (VMHC) disruptions in schizophrenia and their association with gene expression. Using transcription-neuroimaging association analyses, the researchers identified genes linked to VMHC alterations in schizophrenia. The study combined gene expression data from the Allen Human Brain Atlas with case-control VMHC differences from both discovery and replication phases. The results showed that schizophrenia patients exhibited consistent VMHC changes compared to healthy controls, which were correlated with cognitive-related processes. Meta-regression analysis revealed that illness duration was negatively correlated with VMHC abnormalities in the cerebellum and postcentral/precentral gyrus. The abnormal VMHC patterns were stably correlated with 1287 genes enriched for fundamental biological processes such as regulation of cell communication, nervous system development, and cell communication. These genes were overexpressed in astrocytes and immune cells, enriched in extensive cortical regions and wide developmental time windows. The findings suggest that VMHC alterations in schizophrenia are associated with specific genes involved in fundamental biological processes and may contribute to a better understanding of the molecular mechanisms underlying these alterations. The study also explored the association between cognitive-related processes and VMHC alterations using Neurosynth decoding analysis. The results indicate that schizophrenia-related VMHC alterations are linked to cognitive processes such as motivation, reward, and decision-making. The study highlights the importance of gene expression in understanding the neurobiological mechanisms of schizophrenia and provides preliminary evidence for the potential mechanisms underlying VMHC alterations in the disorder. The study has limitations, including the use of data from different individuals for gene expression and rs-fMRI analysis, and the use of adult subjects only for AHBA data. Overall, the study contributes to a more comprehensive understanding of the molecular mechanisms underlying VMHC alterations in schizophrenia.This study investigates homotopic functional connectivity (VMHC) disruptions in schizophrenia and their association with gene expression. Using transcription-neuroimaging association analyses, the researchers identified genes linked to VMHC alterations in schizophrenia. The study combined gene expression data from the Allen Human Brain Atlas with case-control VMHC differences from both discovery and replication phases. The results showed that schizophrenia patients exhibited consistent VMHC changes compared to healthy controls, which were correlated with cognitive-related processes. Meta-regression analysis revealed that illness duration was negatively correlated with VMHC abnormalities in the cerebellum and postcentral/precentral gyrus. The abnormal VMHC patterns were stably correlated with 1287 genes enriched for fundamental biological processes such as regulation of cell communication, nervous system development, and cell communication. These genes were overexpressed in astrocytes and immune cells, enriched in extensive cortical regions and wide developmental time windows. The findings suggest that VMHC alterations in schizophrenia are associated with specific genes involved in fundamental biological processes and may contribute to a better understanding of the molecular mechanisms underlying these alterations. The study also explored the association between cognitive-related processes and VMHC alterations using Neurosynth decoding analysis. The results indicate that schizophrenia-related VMHC alterations are linked to cognitive processes such as motivation, reward, and decision-making. The study highlights the importance of gene expression in understanding the neurobiological mechanisms of schizophrenia and provides preliminary evidence for the potential mechanisms underlying VMHC alterations in the disorder. The study has limitations, including the use of data from different individuals for gene expression and rs-fMRI analysis, and the use of adult subjects only for AHBA data. Overall, the study contributes to a more comprehensive understanding of the molecular mechanisms underlying VMHC alterations in schizophrenia.