We performed comprehensive gene‐expression analysis using the Whole Human Genome 4 x 44K Microarray (Agilent Technologies, Santa Clara, CA, USA). Briefly, we collected tumor cells by macrodissection and performed comprehensive gene‐expression analysis, as previously described.12 Microarray data are available from GSE147571 . Gene‐expression data were analyzed and imaged using GeneSpring GX version 14.5 (Agilent Technologies). The patients with aCRCS were classified into 4 subtypes, A1, A2, B1, and B2, as previously described.12 The numbers of patients in subtype A1 were 39 (12.7%); A2, 107 (34.7%); B1, 105 (34.0%), and B2, 57 (18.5%). CMS analysis11 was performed, as previously described.15 Finally, principal component analysis (PCA) was performed using GeneSpring GX version 14.5 (Agilent Technologies) using the aCRCS gene set.
Genespring gx version 14
Manufactured by Agilent Technologies
Sourced in United States
GeneSpring GX is a software platform for the analysis and visualization of genomic data. Version 14.5.1 provides tools for data import, normalization, and statistical analysis of microarray, RNA-seq, and other high-throughput genomic datasets.
Automatically generated - may contain errors
Lab products found in correlation
5 protocols using genespring gx version 14
1
Comprehensive Gene Expression Analysis of Colorectal Cancer Subtypes
2
CCNDBP1 Gene Expression Profiling
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The SurePrint G3 Human Gene Expression (v2) Microarray Kit (Agilent Technologies, Inc., Santa Clara, CA, USA) and SurePrint G3 Mouse Gene Expression (v2) Microarray Kit (Agilent Technologies, Inc., Santa Clara, CA, USA) GeneSpring GX, version 14.5.1 (Agilent Technologies, Inc., Santa Clara, CA, USA), were used to compare the gene expression levels in mock-transfected cells and in hepatocytes from CCNDBP1-transfected HLE and Ccndbp1 knockout mice and wild mice. There were 6597 of the 26,083 genes in human and 7530 of the 27,122 genes in mice that were clustered hierarchically according to the level of gene expression, with more than two-fold differences in expression. The gene ontology terms were selected on the basis of Fisher’s exact test, followed by the Benjamini–Yekutieli correction method. The expressions in the genes were compared among the groups; genes with more than fivefold differences in expression were shown in the heat map.
3
Molecular Interactions Network Analysis of APM2 Gene Expression
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The SurePrint G3 Human Gene Expression (v2) Microarray Kit (Agilent Technologies, Inc., Santa Clara, CA) and GeneSpring GX, version 14.5.1 (Agilent Technologies, Inc.), were used in comparing the gene expression levels in mock-transfected and APM2-transfected HLE. A total of 6169 genes with more than twofold differences in expression were clustered hierarchically according to the level of gene expression. Ten groups were assessed with related gene expressions using gene ontology term analyses. The gene ontology terms were selected on the basis of Fisher’s exact test, followed by the Benjamini-Yekutieli correction method. To construct a molecular interactions network, the protein–protein association data of the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database21 (link) was imported to Cytoscape22 (link) with the stringApp plugin software. STRING imports protein association knowledge from databases of physical interaction and of curated biological pathway knowledge. From the protein–protein association network, proteins with a cut-off of 0.4 edge confidence score (default value) were selected, and the molecular interaction network was constructed with the default settings in Cytoscape.
4
Transcriptomic Analysis of IQOS CSE Exposure
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At 6 and 24 h after IQOS CSE stimulation, total RNA from ATI-like cells was extracted and purified using RNeasy kit (Qiagen, Hilden, Germany). The samples were run on Agilent SurePrint G3 (Agilent, Santa Clara, CA, USA) and processed as indicated by the manufacturer. Raw signal values were normalized using the 75th percentile and transformed log2 scale. The processed data was analyzed using Genespring GX version 14.9 (Agilent).
5
Comprehensive Microarray Analysis of Liver Transcriptome
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As already described in our previous report (18) , total RNA was extracted from livers and purified. Complementary RNA was generated and labelled with cyanine 3 using a Low Input QuickAmp Labeling Kit (Agilent Technologies) and hybridised to a SurePrint G3 Rat GE microarray 8 × 60K (Agilent Technologies) according to the manufacturer's instructions. Fluorescence signals were detected using Agilent SureScan Microarray Scanner Extraction Software 12.0.3.1 (Agilent Technologies) according to the manufacturer's instructions. Raw data from the Feature Extraction Software were exported to GeneSpring GX version 14.9 (Agilent Technologies). To identify differentially expressed genes in the microarray hybridisation and reduce noise, each data set of fluorescence signals was normalised using a median shift algorithm (shifted to 75 percentile) with background correction to the median of all samples. Only genes with normalised signals detected on all microarrays were judged to be present. Furthermore, genes detected by the multiple probes were selected one to have the largest fold change. Subsequently, in order to find potential associations between the detected hepatic genes and identified metabolites, the Kyoto Encyclopedia of Genes and Genomes pathway database was used.
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