To identify genes that play a critical role in the pathogenesis of NPC, we re-examined the transcriptome data set published in the Gene Expression Omnibus (GSE12452) of NPC tissues (n = 31) versus non-tumorous nasopharyngeal epithelial tissues (n = 10) enriched through laser-capture microdissection for target cells 26 (link)-29 (link). All probe sets were analyzed without filtering or preselection by means of importing raw CEL files of the Affymetrix HUMAN Genome U133 Plus 2.0 microarray platform into Nexus Expression 3 software (BioDiscovery). Supervised functional profiling and comparative analysis were done, as described previously, to identify prominent differentially expressed genes by emphasizing pathways involving glutamate decarboxylase activity in Gene Ontology (GO:0004351) 27 (link)-29 (link). We identified those that with p < 0.01 and a log2-transformed expression fold change > 0.1 for further evaluation.
Nexus expression 3
Manufactured by BioDiscovery
Sourced in United States
The Nexus Expression 3 software is a bioinformatics tool designed for gene expression analysis. It is a comprehensive software package that enables the processing, visualization, and statistical analysis of gene expression data from various high-throughput technologies, such as microarrays and RNA-sequencing.
Automatically generated - may contain errors
Lab products found in correlation
Human genome u133 plus 2.0 microarray platform, by BioDiscovery (6 mentions)
Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (4 mentions)
Genechip human genome u133 plus 2.0 array, by Thermo Fisher Scientific (3 mentions)
Ingenuity pathway analysis (ipa), by Qiagen (3 mentions)
Human genome u133 plus 2.0 array terrace, by Thermo Fisher Scientific (2 mentions)
Human genome u133 plus 2, by Thermo Fisher Scientific (2 mentions)
Genespring 12, by Agilent Technologies (2 mentions)
Rneasy lipid tissue mini kit, by Qiagen (2 mentions)
Humanht 12 v3.0 expression beadchip, by Illumina (1 mentions)
Nexus software, by BioDiscovery (1 mentions)
Humanht 12 expression beadchip, by Illumina (1 mentions)
Human genome u133 plus 2.0 array platform, by Thermo Fisher Scientific (1 mentions)
Genechip human genome u133 plus 2.0 array platform, by Thermo Fisher Scientific (1 mentions)
Nexus expression 3 statistical software, by BioDiscovery (1 mentions)
Human genome u133 plus 2.0 microarray platform, by Thermo Fisher Scientific (1 mentions)
Hg u133 plus 2 array, by Thermo Fisher Scientific (1 mentions)
Prism 7, by GraphPad (1 mentions)
Nexus copy number 8, by BioDiscovery (1 mentions)
Agilent sureprint g3 rat ge 8 60 k microarrays, by Agilent Technologies (1 mentions)
53 protocols using nexus expression 3
1
Identifying Critical Genes in NPC Pathogenesis
2
Transcriptomic Analysis of Lipid Biosynthesis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
We first analyzed one public transcriptome dataset (GSE31684) that was obtained from the NIH Gene Expression Omnibus. For the data analysis, the raw CEL files available in the Affymetrix HUMAN Genome U133 Plus 2.0 microarray platform were imported into Nexus Expression 3 software (BioDiscovery) to analyze all probe sets without using pre-selection or filtering, as previously described 7 (link)-10 (link). Supervised comparative analyses and functional profiling were performed to identify significantly differentially expressed genes, and special attention was paid to pathways known to be involved in lipid biosynthetic process in Gene Ontology (GO:0008610). Those genes with P < 0.01 and log2-transformed expression fold change >±0.1 were chosen and the gene with most significant P value and the highest log2-transformed fold-change in expression was selected for further validation. To cross-validate the findings, the transcriptomic data from another dataset (GSE32894), which was generated using an Illumina HumanHT-12 V3.0 expression bead chip, was also analyzed.
3
Identifying Prognostic Tyrosine Kinase Genes in Bladder Cancer
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
By performing data mining on the Gene Expression Omnibus database (National Center Biotechnology Information), we identified data set GSE31684 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc¼GSE31684 ) and investigated 93 UBUC specimens using the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. We imported the raw files into and computed the expression levels identified by probe sets, without preselection or filtering, using Nexus Expression 3 software (BioDiscovery, EI Segundo, CA, USA). We carried out a supervised comparative analysis to inspect the differentially-expressed genes with statistical significance according to the primary tumor status and metastatic status. We focused on the functional profiles of transcriptions associated with transmembrane receptor tyrosine kinase activity (GO:0004714). Further survival analysis was performed in all cases by dichotomize cases into high- and low-expression clusters in an unsupervised manner to computerize the prognostic impact of selected gene.
4
Lipid Metabolism Drivers in Stromal Tumors
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Focusing on driver(s) deregulated in lipid metabolism, we reappraised transcriptomic dataset of imatinib-naïve gastric and intestinal stromal tumors at various risk levels to search for aberrantly expressed genes critical in tumor progression. These samples were deposited in Gene Expression Omnibus (GSE8167) and profiled for global mRNA expression by using GeneChip Human Genome U133 Plus 2.0 arrays. The raw CEL files were imported into the Nexus Expression 3 software (BioDiscovery Hawthorne, CA, USA) to analyze all probe sets without preselection or filtering. Unsupervised comparative analysis was performed to identify significant genes differentially expressed between the high-risk and non-high-risk samples, with special attention paid to the lipid metabolic process in Gene Ontology (GO: 0006629). The ranking in the expression fold change (at least >1-fold in the log2-transformed ratio) and the power of statistical significance (p ≤ 0.0001 according to the Student t test) were considered for prioritizing potential candidate genes for further validation.
5
Transcriptomic Analysis of NPC Carcinogenesis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To find genes associated with the carcinogenesis of NPC, we analyzed the transcriptomic dataset deposited in the Gene Expression Omnibus database (GSE12452), consisting of 31 NPC tissues and 10 non-neoplastic nasopharyngeal mucosal epithelial tissues enriched by laser capture microdissection for cells of interest 7 (link). We used Nexus Expression 3 software (BioDiscovery) to analyze the raw CEL files of the Affymetrix HUMAN Genome U133 Plus 2.0 microarray platform. All probe sets were analyzed without pre-selection or filtering. We performed supervised comparative analysis to find genes that have significantly different expression, particularly focusing on those related to cyclin-dependent protein kinase activity (GO: 0000079). While comparing tumor versus non-tumor tissues or low-staged versus high-staged cases, those with P<0.01 and log2-transformed expression fold change >0.1 were selected for further analysis.
6
Profiling DNA Copy Number Alterations in Myxofibrosarcoma
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Nexus software (BioDiscovery) was employed to reappraise our previously reported genomic profiling data (GSE35483) of myxofibrosarcoma tissue and cell line samples for profiling the DNA copy number alterations across the whole genome and identifying altered genes within imbalanced chromosomes in a zoomed-in view 6 (link), 11 (link). Apart from previously reported 5p gain, an additional gained region was mapped to chromosome 11q, specifically 11q13.5-14.1 region, where several oncogenes were previously described to be amplified in common carcinomas 20 (link), 21 (link). Hence, candidates in the published transcriptomic datasets (GSE21122) were further screened for those exhibiting differential mRNA expression between myxofibrosarcomas and non-neoplastic soft tissues 5 (link), given that genes with concordant alterations in the genomic and expression profiling represent potential drivers leading to myxofibrosarcoma pathogenesis. The raw CEL files obtained from Affymetrix U133A microarray platform were then imported into Nexus Expression 3 software (BioDiscovery) to analyze all probe sets without pre-selection or filtering. Those genes with p<0.001 were considered significant.
7
Identifying Pivotal Genes in Urothelial Carcinoma
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To identify genes pivotal in pathogenesis and tumor invasiveness in UC, data mining by use of the GEO (National Center Biotechnology information, Bethesda, MD, USA) was done. One dataset, GSE32894 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894 ) analyzing radical cystectomy tissues from 308 UBUCs by the use of v3.0 of Illumina HumanHT-12 expression beadchip, was recognized. The raw CEL files that were imported into Nexus Expression 3 software (BioDiscovery) were utilized to computerize the expression level. There was no preselection or filtering in all probe sets for the analysis. We used supervised comparative analysis and functional profiles to analyze which transcripts were differentially expressed with statistical significance, focusing on pathways associated with positive regulation of tyrosine phosphor-STAT5 (GO:0042523), based on primary tumor status (pT) and distant metastasis. Those differentially expressed between high-stage (pT2-pT4) UC with metastasis and low-stage (pTa-pT1) UC without metastasis was compared for further analysis. Genes with significantly differential expression (p<0.001) were chosen. All enrolled 308 cases were dichotomized to high- and low-expression clusters for further survival analysis to computerize the potential valuable prognosticators of selected genes.
8
Identifying DEGs Linked to CCRT Response
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
We explored the DEGs correlated to CCRT response in a gene expression omnibus (GEO) dataset (GSE35452), including 46 patients with rectal cancer. Before starting preoperative CCRT, biopsy specimens were collected during colonoscopy and analyzed using the Affymetrix Human Genome U133 Plus 2.0 Array [23 (link)]. To computerize the gene expression levels, we imported raw CEL files into the Nexus Expression 3 software (BioDiscovery, El Segundo, CA, USA). According to the clinical response to CCRT, we compared “responders” and “nonresponders” to identify significant DEGs related to Rho guanyl-nucleotide exchange factor activity (GO:0005085). DEGs with p < 0.01 and log2 ratio > 0.15 were chosen for further evaluation.
9
Identifying Critical Genes in Nasopharyngeal Carcinoma
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To identify critical genes in the pathogenesis of NPC, we reappraised the transcriptome dataset deposited in Gene Expression Omnibus (GDS3610) of NPC tissues (n=25) versus non-neoplastic nasopharyngeal mucosal epithelial tissues (n=3) enriched by laser capture microdissection of the cells of interest (Fig. 1 ). We analyzed the gene expression levels by importing the raw CEL files of the Affymetrix HUMAN Genome U133 Plus 2.0 microarray platform into Nexus Expression 3 software (BioDiscovery) as previously described 12 -14 (link). All probe sets were tested without pre-selection or filtering. Supervised comparative analysis and functional profiling were performed to identify significant differentially expressed genes associated with the regulation of transcription from the RNA polymerase II promoter in the transcriptome of NPCs. Those with p<0.01 and log2-transformed expression fold-change >1 were selected for further analysis. Among the statistically significant genes, HOXC6 appeared as the top ranking differentially expressed candidate (Table 1 ), prompting us to further characterize the immunoexpression level of HOXC6 in the NPC cohort.
10
Differential Expression Analysis of Cell Adhesion Genes in Nasopharyngeal Carcinoma
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
We selected mRNA expression datasets from the gene expression omnibus database (National Center for Biotechnology Information, Bethesda, MD), from which we obtained and analyzed the transcriptome dataset (GSE12452). The GSE12452 dataset included 31 NPC tissues and 10 nonneoplastic nasopharyngeal mucosal epithelial tissue samples. Using Nexus Expression 3 software (BioDiscovery, USA) and the Affymetrix Human Genome U133 Plus 2.0 Array terrace to obtain the original files, we calculated the expression degrees of genes by probe combinations. The probe combination was resolved without preselection or filtration. Through an inspected comparative analysis, genes that were expressed in the dataset were intersected to identify the most significant genes. We searched for genes with significant differential expression (log2 ratio > 2, P < .01), focusing on genes related to cell adhesion (GO:0003779).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!