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Genome Information for Homo sapiens
Gene expression profiles were generated from muscle biopsies from 134 individuals, and differences in expression based on sex were explored.
Top differentially expressed gene lists are often inconsistent between studies and it has been suggested that small sample sizes contribute to lack of reproducibility and poor prediction accuracy in discriminative models. We considered sex differences (69♂, 65♀) in 134 human skeletal muscle biopsies using DNA microarray. The full dataset and subsamples (n= 10 (5♂, 5♀) to n=120 (60♂, 60♀)) thereof were used to assess the effect of sample size on the differential expression of single genes, gene rank order and prediction accuracy. Using our full dataset (n=134), we identified 717 differentially expressed transcripts (p-value < 0.0001; false discovery rate < 0.006) and we were able to predict sex with 92% accuracy, both within our dataset and on external datasets. Both p-values and rank order of top differentially expressed genes became more variable using smaller subsamples. For example, at n=10 (5♂, 5♀), no gene was considered differentially expressed at p<0.0001 and prediction accuracy was ~50% (no better than chance). We found that sample size clearly affects microarray analysis results; small sample sizes result in unstable gene lists and poor prediction accuracy. We anticipate this will apply to other phenotypes, in addition to sex.
Overall design: RNA was isolated from 134 muscle samples. Gene expression is compared between males and females.
Accession | PRJNA178029; GEO: GSE41726 |
Data Type | Transcriptome or Gene expression |
Scope | Multiisolate |
Organism | Homo sapiens[Taxonomy ID: 9606] Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo; Homo sapiens |
Publications (total 4) Less... | - Anoveros-Barrera A et al., "Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression.", Skelet Muscle, 2019 Sep 14;9(1):24
More...- Anoveros-Barrera A et al., "Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression.", Skelet Muscle, 2019 Sep 14;9(1):24
- Anoveros-Barrera A et al., "Clinical and biological characterization of skeletal muscle tissue biopsies of surgical cancer patients.", J Cachexia Sarcopenia Muscle, 2019 Dec;10(6):1356-1377
- Johns N et al., "New genetic signatures associated with cancer cachexia as defined by low skeletal muscle index and weight loss.", J Cachexia Sarcopenia Muscle, 2017 Feb;8(1):122-130
- Stretch C et al., "Effects of sample size on differential gene expression, rank order and prediction accuracy of a gene signature.", PLoS One, 2013;8(6):e65380
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Submission | Registration date: 19-Oct-2012 Oncology, University of Alberta |
Relevance | Medical |
Project Data:
Resource Name | Number of Links |
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Publications |
PubMed | 4 |
PMC | 4 |
Other datasets |
GEO DataSets | 1 |
GEO Data DetailsParameter | Value |
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Data volume, Spots | 5494000 |
Data volume, Processed Mbytes | 125 |
Data volume, Supplementary Mbytes | 1167 |