The two datasets GSE3585 and GSE5406 were loaded onto the GPL96 platform (Affymetrix Human Genome U133A Array [HG-U133A]). Additionally, the series matrix and platform annotation for the two databases were downloaded from the GEO database. The probe identity documents were transformed into gene symbols. Then, via the R package “Surrogate Variable Analysis,” the two databases were merged, and any batch effect was removed using the “Empirical Bayes” method[21 (link)]. The R package “limma” was applied to identify the DEGs between the DCM and healthy myocardium tissues[22 (link)]. The screening criteria were set as P < 0.05 and |log fold change (FC)| > 0.589 (FC > 1.5). Volcano and heat maps were generated using R software.
Human genome u133a array hg u133a
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The Human Genome U133A Array (HG-U133A) is a high-density oligonucleotide array designed for the detection and analysis of gene expression. It contains over 22,000 probe sets representing approximately 18,400 human genes. The array is commonly used in genetic research and expression profiling studies.
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6 protocols using human genome u133a array hg u133a
1
Differential Gene Expression Analysis of DCM
2
Comparative Analysis of Ischemic Cardiomyopathy
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Two microarray-based gene expression profiling datasets are downloaded from the NCBI GEO database [13 (link)]. Both datasets GSE5406 [14 (link)] and GSE1869 [15 (link)] profiled ischemic cardiomyopathy samples and their controls on the Affymetrix Human Genome U133A Array (HG-U133A) platform. The transcriptomes are normalized using the RMA algorithm [16 (link)]. The gene expression profiles of ischemic cardiomyopathy samples and the nonfailing controls are kept for binary classification study in this work.
3
Comparative Transcriptomic Analysis of Cervical and Endometrial Cancers
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Raw microarray data of CC (GSE9750, GSE7803, GSE63514) and EC (GSE17025, GSE115810, GSE36389) were downloaded from the GEO database (Table 1 ). In the six datasets of our study, GSE9750, GSE7803, GSE115810, and GSE36389 were processed using the GPL96 platform (Affymetrix Human Genome U133A Array, HG-U133A, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL96 , accessed on 3 July 2021), while GSE63514 and GSE17025 were based on GPL570 platform (Affymetrix Human Genome U133 Plus 2.0 Array, HG-U133_Plus_2, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570 , accessed on 3 July 2021). The detailed information of datasets is as follows: GSE9750 included 33 cervical tumor and 24 normal tissue samples. GSE7803 covered 21 cervical tumor and 10 normal tissue samples. GSE63514 included data from 28 cervical tumor and 24 normal samples. GSE17025 covered 91 endometrial tumor and 12 normal tissue samples. GSE115810 comprised 24 endometrial tumor and 3 normal samples. GSE36389 consisted of 13 endometrial tumor and 7 normal samples.
4
LINCS L1000 Gene Expression Data
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Publicly available LINCS L1000 level three data (q2norm) were downloaded from lincscloud (http://www.lincscloud.org ) with permission. Gene knockdown expression data generated from breast cancer cell line MCF7 were used for correspondence. This dataset contains 53,763 gene expression profiles involving 12,792 RNAi reagents targeting 3689 genes and 2922 untreated profiles on 165 plates as control (Supplementary Materials Table S2 ). The L1000 technology originally measures expressions of 978 landmark genes to infer the entire transcriptome via linear regression. Each profile in LINCS contains 22,268 probe sets, which roughly correspond to the Affymetrix Human Genome U133A Array (HG-U133A).
5
Metastatic Potential in TSCC Cells
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mRNA expression profiles of three pairs of TSCC cell lines with different metastatic potential (SCC9 cells transfected with miR-138 mimic vs those transfected with control mimic, UM1 cells transfected with miR-138 mimic vs those transfected with control mimic and UM2 cells vs UM1 cells) were determined. Human Genome U133A Array (HG U133A, Affymetrix, Santa Clara) was used for gene expression analysis as previously reported [32 (link)].
6
Diffuse Large B-Cell Lymphoma Microarray Analysis
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Gene expression microarray data and clinical information for DLBCL were downloaded from the Gene Expression Omnibus (GEO) database. Affymetrix gene expression profiles were performed using Affymetrix Human Genome U133 Plus 2.0 (HG-U133 Plus_2.0) for 2 cohorts of patients (GSE31312 and GSE10846) and using Affymetrix Human Genome U133A Array (HG-U133A) for 1 cohort of patients (GSE4475). After removing patients with no clinical or subtype information, a total of 905 DLBCL patients were included in our study (Table 1 ), comprising 426 patients from Visco’s study (the accession number is GSE31312) [10 (link)], 350 patients from Lenz’s study (the accession number is GSE10846) [25 (link)] and 129 patients from Hummel’s study (the accession number is GSE4475) [26 (link)].
Clinical and pathological characteristics of patients with DLBCL in our study
| Characteristics | Discovery cohort | Internal validation cohort | GSE31312 cohort | GSE10846 cohort | GSE4475 cohort |
|---|---|---|---|---|---|
| No. of patients | 213 | 213 | 426 | 350 | 129 |
| Age, year | |||||
| >60 | 121 | 123 | 244 | 196 | 72 |
| ≤60 | 92 | 90 | 182 | 154 | 57 |
| Gender | |||||
| Female | 101 | 82 | 183 | 152 | 54 |
| Male | 112 | 131 | 243 | 184 | 74 |
| Unknown | 14 | 1 | |||
| Stage | |||||
| I/II | 97 | 106 | 203 | 160 | 36 |
| III/IV | 116 | 107 | 223 | 184 | 48 |
| Unknown | 6 | 45 | |||
| No. of extranodal sites | |||||
| <2 | 167 | 170 | 337 | 299 | |
| ≥2 | 46 | 43 | 89 | 26 | |
| Unknown | 25 | ||||
| LDH | |||||
| 0 | 72 | 61 | 133 | 140 | |
| 1 | 120 | 133 | 253 | 156 | |
| Unknown | 21 | 19 | 40 | 54 | |
| ECOG | |||||
| <2 | 168 | 171 | 339 | 256 | |
| ≥2 | 45 | 42 | 87 | 74 | |
| Unknown | 20 | ||||
| Subtype | |||||
| GCB | 106 | 121 | 227 | 183 | 74 |
| ABC | 107 | 92 | 199 | 167 | 55 |
| Unclassified | |||||
| Survival status | |||||
| Dead | 80 | 74 | 154 | 143 | 51 |
| Alive | 133 | 139 | 272 | 207 | 42 |
| Unknown | 36 | ||||
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