Gene expression profile exploration of a large dataset on chronic fatigue syndrome.
OBJECTIVE
To gain understanding of the molecular basis of chronic fatigue syndrome (CFS) through gene expression analysis using a large microarray data set in conjunction with clinically administrated questionnaires.


METHODS
Data from the Wichita (KS, USA) CFS Surveillance Study was used, comprising 167 participants with two self-report questionnaires (multidimensional fatigue inventory [MFI] and Zung depression scale [Zung]), microarray data, empiric classification, and others. Microarray data was analyzed using bioinformatics tools from ArrayTrack.


RESULTS
Correspondence analysis was applied to the MFI questionnaire to select the 23 samples having either the most or the least fatigue, and to the Zung questionnaire to select the 26 samples having either the most or least depression; ten samples were common, resulting in a total of 39 samples. The MFI and Zung-based CFS/non-CFS (NF) classifications on the 39 samples were consistent with the empiric classification. Two differentially-expressed gene lists were determined, 188 fatigue-related genes and 164 depression-related genes, which shared 24 common genes and involved 11 common pathways. Principal component analysis based on 24 genes clearly separates 39 samples with respect to their likelihood to be CFS. Most of the 24 genes are not previously reported for CFS, yet their functions are consistent with the prevailing model of CFS, such as immune response, apoptosis, ion channel activity, signal transduction, cell-cell signaling, regulation of cell growth and neuronal activity. Hierarchical cluster analysis was performed based on 24 genes to classify 128 (=167-39) unassigned samples. Several of the 11 identified common pathways are supported by earlier findings for CFS, such as cytokine-cytokine receptor interaction and neuroactive ligand-receptor interaction. Importantly, most of the 11 common pathways are interrelated, suggesting complex biological mechanisms associated with CFS.


CONCLUSIONS
Bioinformatics is critical in this study to select definitive sample groups, analyze gene expression data and gain insight into biological mechanisms. The 24 identified common genes and 11 common pathways could be important in future studies of CFS at the molecular level.
Fang
Hong
H
Z-Tech Corporation at NCTR, Division of Bioinformatics, 3900 NCTR Road, Jefferson, AR 72079, USA.
Xie
Qian
Q
Boneva
Roumiana
R
Fostel
Jennifer
J
Perkins
Roger
R
Tong
Weida
W
D000328:Adult; D017209:Apoptosis / Q000235:genetics / Q000502:physiology; D016000:Cluster Analysis; D019295:Computational Biology; D016207:Cytokines / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D003863:Depression / Q000523:psychology; D015673:Fatigue Syndrome, Chronic / Q000453:epidemiology / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007473:Ion Channels / Q000235:genetics / Q000502:physiology; D008024:Ligands; D020411:Oligonucleotide Array Sequence Analysis; D025341:Principal Component Analysis; D011569:Psychiatric Status Rating Scales; D018121:Receptors, Cytokine / Q000235:genetics / Q000502:physiology; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology
D016207:Cytokines; D007473:Ion Channels; D008024:Ligands; D018121:Receptors, Cytokine