  The disruption of circadian rhythm is a cardinal symptom for Alzheimer's
disease (AD) patients. The full circadian rhythm orchestration of gene
expression in the human brain and its inherent associations with AD remain
largely unknown. We present a novel comprehensive approach, PRIME, to detect
and analyze rhythmic oscillation patterns in untimed high-dimensional gene
expression data across multiple datasets. To demonstrate the utility of PRIME,
firstly, we validate it by a time course expression dataset from mouse liver as
a cross-species and cross-organ validation. Then, we apply it to study
oscillation patterns in untimed genome-wide gene expression from 19 human brain
regions of controls and AD patients. Our findings reveal clear, synchronized
oscillation patterns in 15 pairs of brain regions of control, while these
oscillation patterns either disappear or dim for AD. It is worth noting that
PRIME discovers the circadian rhythmic patterns without requiring the sample's
timestamps. The codes for PRIME, along with codes to reproduce the figures in
this paper, are available at https://github.com/xinxingwu-uk/PRIME.
