We accessed the public functional genomics data repository, Gene Expression Omnibus (GEO), at the National Center for Biotechnology Information. GSE6004 comprises gene expression data of seven paired central and invasion regions of papillary thyroid cancer, as well as four normal tissues [10 (link)]. Expression profiling was performed using the Affymetrix Human Genome U133 Plus 2.0 microarray platform (Affymetrix; Thermo Fisher Scientific, Santa Clara, CA, USA). Reported somatic mutations of the SMARCB1 gene were explored using the Catalogue of Somatic Mutations in Cancer (COSMIC) at the Wellcome Sanger Institute [11 (link)].
Human genome u133 plus 2.0 microarray platform
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Human Genome U133 Plus 2.0 microarray platform is a high-density oligonucleotide array designed to analyze the expression of over 47,000 transcripts and variants, representing approximately 39,000 well-characterized human genes. It is a comprehensive tool for whole-genome expression analysis.
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4 protocols using human genome u133 plus 2.0 microarray platform
1
Transcriptional Profiling of Papillary Thyroid Cancer
2
Identifying Key Genes in Nasopharyngeal Carcinoma
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To identify the key genes that play critical roles in NPC, we reanalyzed the NPC dataset published in GEO (GSE12452), which contains 10 nontumor nasopharyngeal epithelial tissue samples and 31 NPC tissue samples [22 (link)–24 (link)]; and GSE64634, which contains four normal nasopharyngeal tissue samples and 12 nasopharyngeal carcinoma specimens [25 (link)]. Briefly, raw CEL files from the Affymetrix Human Genome U133 Plus 2.0 microarray platform were downloaded and imported, along with the 32 GSM samples, into R (version 3.6). Gene expression levels were then analyzed, and differentially expressed genes were identified using the limma package [26 (link)]. Data were then plotted in a volcano plot with P < 0.01 and a log2-transformed expression fold change >1.0 for further evaluation.
3
Investigating Oral SCC Tumorigenesis
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From the publicly available GEO database, we downloaded the oral SCC dataset (GSE37991) which includes 40 patients with tumor and non-tumor pair-wise samples 12 (link). We analyzed the raw data on the Affymetrix HUMAN Genome U133 Plus 2.0 microarray platform and included all sets of probes, trying to find genes associated with tumorigenesis of oral SCC. We performed comparative analysis to find genes that have different expressions between the tumors and non-tumors, particularly focusing on genes related to AMACR activity (GO:0008111). Under the initial analysis of gene expression, those with P<0.01 and log2-transformed expression fold change >0.1 were selected for further analysis. The result was presented as heat map.
4
Transcriptomic Profiling of Rectal Cancer Response
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In the NCBI GEO public transcriptomic database (GSE35452), information from 46 rectal cancer patients who had undergone preoperative chemoradiation was used for data mining. To quantify the expression levels, the raw. cel files on the Affymetrix Human Genome U133 Plus 2.0 microarray platform (Affymetrix, Inc., Santa Clana, CA, USA) were analyzed using the Nexus Expression 3 (BioDiscovery, Hawthorne, CA, USA) software, employing a comparative analysis without filtering or preselection. According to the response to preoperative chemoradiation, the samples were separated into “responders” and “nonresponders”, with special attention given to the genes involved in intracellular protein transport (GO:0006886). Transcripts with p < 0.01 and an expression fold change > ±0.1 log2 ratio were selected for analysis.
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