Table 1 Examples of some transcriptomic studies classified according to the three different methods described (#1, DEGs; #2, WGCNA; # 3, DEGs + WGNCA; # 1 + 2 indicates the use of both methods, without combining them, as in #3) to analyze transcriptomic data since the development of WGCNA in 2005
From: Improved biomarker discovery through a plot twist in transcriptomic data analysis
Method # | Species | Cell type/ tissue | Technology | Reference |
|---|---|---|---|---|
1 | Rattus norvegicus | Gonads | Microarray | [9] |
1 | Setaria italica L | Plant seeds | SSH | [11] |
1 | Gallus gallus | Gonads | RNA-seq | [33] |
1 | Trachemys scripta | Embryos | RNA-seq | [15] |
1 | Triticum aestivum L | Plant seeds | Microarray | [14] |
1 | Homo sapiens | Breast | RNA-seq | [12] |
1 | Xenopus laevis | Gonads | Microarray | [34] |
1 | Rattus norvegicus | Brain | RNA-seq | [10] |
1 | Dicentrarchus labrax | Gonads | Microarray | [35] |
2 | Homo sapiens | Brain | Microarray | [36] |
2 | Homo sapiens | Brain | Microarray | [37] |
2 | Homo sapiens | Brain | RNA-seq | [19] |
2 | Homo sapiens | Bone | Microarray | [38] |
2 | Homo sapiens | Liver | Microarray | [39] |
2 | Mus musculus | Placenta | Microarray | [40] |
2 | Homo sapiens | Brain | Microarray | [41] |
2 | Oplegnathus fasciatus | Spleen | RNA-seq | [42] |
2 | Homo sapiens | Blood | RNA-seq | [43] |
2 | Homo sapiens | Lung | Microarray | [44] |
2 | Homo sapiens | Bladder | RNA-seq | [20] |
3 | Homo sapiens | Bladder | Microarray | [45] |
3 | Homo sapiens | Colon mucose | Microarray | [46] |
3 | Homo sapiens | Podocyte cells | Microarray | [47] |
3 | Bubalus bubalis | Mammary gland | RNA-seq | [48] |
3 | Homo sapiens | Bladder | Microarray | [49] |
3 | Homo sapiens | Lung | Microarray | [50] |
3 | Homo sapiens | Bladder | RNA-seq | [51] |
3 | Bubalus bubalis | Blood | RNA-seq | [52] |
3 | Homo sapiens | Brain | RNA -seq | [53] |
3 | Homo sapiens | Liver | RNA-seq | [54] |
3 | Scophthalmus maximus | Gill | RNA-seq | [55] |
3 | Scophthalmus maximus | Kidney | RNA-seq | [56] |
3 | Homo sapiens | Breast | Microarray | [57] |
3 | Rattus norvegicus | Spinal cord | RNA-seq | [58] |
3 | Homo sapiens | Stem cells | RNA-seq | [59] |
3 | Bos taurus | Blood | RNA-seq | [60] |
1 + 2 | Scophthalmus maximus | Gonads | Microarray | [13] |
1 + 2 | Paralichthys olivaceus | Embryo | RNA-seq | [25] |
1 + 2 | Homo sapiens | Brain | RNA-seq | [26] |
1 + 2 | Gallus gallus | Lung | RNA-seq | [27] |
1 + 2 | Homo sapiens | Organoids | RNA-seq | [28] |
1 + 2 | Homo sapiens | Placenta | Microarray | [29] |
1 + 2 | Mus musculus | Gonads | RNA-seq | [30] |
1 + 2 | Homo sapiens | Lung | RNA-seq | [31] |
1 + 2 | Mus musculus | Pancreas | Microarray | [32] |