Table 3.
Analysis and comparison of gene expression data sets available in the GEO database
| Reference | GEO Number | Platform | Tissue | n/group | FC | P | FDR |
|---|---|---|---|---|---|---|---|
| Post vs. PreRYGB Surgery | |||||||
| 1 | GSE48452 | Affymetrix Human Gene 1.1 ST | Liver | 19, 14 | −1.249 | 0.003 | 0.077 |
| 3 | GSE19790 | Illumina human-6 v2.0 expression beadchip | Whole blood | 11 | −1.128 | 0.472 | 1.000 |
| 18 | GSE32575 | Illumina human-6 v2.0 expression beadchip | Monocytes | 18 | 1.152 | 0.019 | 0.035 |
| 38 | GSE5109 | Affymetrix Human Genome U133 Plus 2.0 | Muscle (vastus lateralis) | 3 | −1.479 | 0.201 | 0.945 |
| 2 | GSE45747 | Illumina Genome Analyzer IIx | Muscle (vastus lateralis) | 5 | −1.157 | 0.668 | 0.808 |
| 17 | GSE29411 | Affymetrix Human Genome U133 Plus 2.0 | Omental and subcutaneous adipose tissue | 10 | 1.190 | 0.598 | 0.893 |
| N/A | GSE72158 | Illumina Human HT-12 V4.0 expression beadchip | Subcutaneous adipose tissue | 42 | −1.364 | 0.000 | 0.000 |
| 37 | GSE53378 | Affymetrix Human Gene 2.0 ST | Subcutaneous adipose tissue | 16 | −1.088 | 0.092 | 0.364 |
| Obesity vs. Normal Body Weight | |||||||
| 36 | GSE48964 | Affymetrix Human Gene 1.0 ST | Adipose tissue stem cells | 3 | 1.052 | 0.492 | 0.787 |
| 24 | GSE2508 | Affymetrix Human Genome U95A to U95E and U95 Version 2 | Subcutaneous adipose tissue | 9, 10 | 1.397 | 4.268 | 0.000 |
| N/A | GSE48521 | Affymetrix Human Genome U133 Plus 2.0 | Amniotic fluid | 8 | 1.164 | 0.501 | 0.989 |
| 21 | GSE10946 | Affymetrix Human Genome U133 Plus 2.0 | Luteinized cumulus cells | 12, 11 | 1.057 | 0.871 | 1.000 |
| 9 | GSE53232 | Affymetrix Human Gene 1.1 ST | Immune cells: peripheral blood mononuclear cells | 60, 68 | 1.045 | 0.012 | 0.316 |
| 42 | GSE45233 | Illumina HumanHT-12 V4.0 expression beadchip | (injured) Meniscus | 4 | −1.108 | 0.618 | 0.935 |
| N/A | GSE73034 | Agilent-014850 Whole Human Genome | Muscle | 21, 7 | 1.158 | 0.117 | 0.597 |
| Microarray 4x44K G4112F | |||||||
| N/A | GSE15524 | CodeLink UniSet Human 20K I Bioarray | Omental and subcutaneous adipose tissue | 21, 7 | −1.267 | 0.440 | 0.961 |
| 34 | GSE2510 | Affymetrix Human Genome U133A and U133B | Primary culture abdominal subcutaneous preadipocytes | 14 | −1.065 | 0.462 | 0.925 |
| 40 | GSE22435 | Affymetrix Human Genome U133 Plus 2.0 | Muscle (rectus abdominis) | 10 | −1.011 | 0.942 | 0.989 |
| 46 | GSE26637 | Affymetrix Human Genome U133 Plus 2.0 | Subcutaneous adipose tissue | 5 | 1.199 | 0.319 | 0.790 |
| 33 | GSE12050 | INSERM-Agilent-012391 Whole Human Genome Oligo Microarray G4112A | Subcutaneous adipose tissue | 9 | −1.059 | 0.486 | 0.624 |
| 49 | GSE29718 | Affymetrix Human Gene 1.0 ST | Subcutaneous and visceral adipose tissue | 10 | 1.114 | 0.350 | 0.961 |
| 8 | GSE60403 | Affymetrix Human Genome U133 Plus 2.0 | Umbilical cord Blood | 8 | 1.037 | 0.783 | 0.966 |
| N/A | GSE73078 | Agilent-039494 SurePrint G3 Human GE v2 8×60K Microarray 039381 | Muscle (vastus lateralis) | 10 | 1.040 | 0.750 | 0.932 |
| 14 | GSE18897 | Affymetrix Human Genome U133 Plus 2.0 | Whole blood | 20 | −1.735 | 0.007 | 0.050 |
| 39 | GSE15653 | Affymetrix Human Genome U133 Plus 2.0 | Liver | 13, 5 | 1.014 | 0.974 | 0.988 |
| 12 | GSE63067 | Affymetrix Human Genome U133 Plus 2.0 | Liver | 9, 7 | 1.046 | 0.676 | 0.941 |
| 28 | GSE37031 | Affymetrix Human Genome U133 Plus 2.0 | Liver | 8, 7 | −1.212 | 0.132 | 0.487 |
| 26 | GSE24807 | GE Healthcare / Amersham Biosciences CodeLink Human Whole Genome Bioarray | Liver | 12, 5 | −1.113 | 0.676 | 0.828 |
Gene expression data sets include the gene expression profile of any available tissue and compare the following groups: 1) obesity vs. normal body weight, 2) pre- vs. post-gastric bypass surgery, and 3) normal liver vs. NAFLD. There was no study with probes specific only for NCBI Reference Sequence NM_002654 (PKM gene transcript variant 1 or PKM2). FC, fold change; P, P value; FDR, false discovery rate.