The Pathway enrichment analysis was conducted using GeneGo MetaCore Software (Version 6.31 build 68930, Thomson Reuters). Significantly enriched biological processes and pathways were called by using a FDR value of less than 0.1. The p value and FDR were calculated for each pathway map in iFTSEC283 and iOSE11 cells for upregulated and downregulated differentially expressed genes.
Genego metacore software
Manufactured by Thomson Reuters
Sourced in United States
GeneGo MetaCore software is a comprehensive, manually curated database of human protein-protein, protein-DNA, and protein-compound interactions, signaling, and metabolic pathways. It provides tools for the analysis of high-throughput data, such as gene expression, proteomics, metabolomics, and screening data.
Automatically generated - may contain errors
7 protocols using genego metacore software
1
Pathway Enrichment Analysis of Differential Gene Expression
2
Epigenetic Profiling and Age Estimation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Statistical analysis was performed in R v4.0.4. The Kruskal–Wallis test, followed by Dunn’s test and Bonferroni correction, was used for comparing groups. Fischer’s exact test followed by Bonferroni correction was used to compare the distribution of DM-CpGs on each chromosome. A heatmap was created by the ComplexHeatmap package44 (link). Epigenetic age was estimated with Horvath’s pan-tissue clock22 (link), the PhenoAge clock23 (link), and the epiTOC clock24 (link), and the epigenetic ages were then adjusted for chronological age and estimated granulocyte proportion. Gene ontology analysis was performed with the GeneGO MetaCore™ software (Thomson Reuters, New York, NY) using the enrichment analysis workflow tool. The analysis was based on genes with DM-CpGs with |Δβ|≥ 0.2 and the results were presented as gene ontology (GO) processes by the MetaCore software. Epigenetic regulation of gene expression pathways was retrieved from the Reactome pathway knowledgebase (Epigenetic regulation of gene expression (Homo sapiens), R-HSA-212165)45 .
3
Pathway and Interaction Analysis of Glioma Proteins
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
After identifying the significant proteins from various comparisons, we proceeded further for the identification of enriched pathways and gene ontology terms using GeneGoMetacore™ software (Thomson Reuters). The significance level of 0.05 was used for this analysis and FDR corrected values at p < 0.05 were used as a threshold for these analysis. We, further, wanted to investigate the protein-protein interactions among the significant proteins identified from various grades of gliomas for which we used QIAGEN’s Ingenuity®Pathway Analysis (IPA®, QIAGEN Redwood City, www.qiagen.com/ingenuity ).
4
Kinase Cascades and Transcription Factors
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The differentially regulated (≥1.5 increase with p < 0.05) coding transcripts identified in PMA and A23187 at 30- and 60-min time points were used for building kinase cascades, transcription factors and related gene interaction networks using Ingenuity Pathways Analysis (IPA) software (Ingenuity Systems, Redwood City, CA) and GeneGo Metacore software (Thomson Reuters, St. Joseph, MI, USA).
5
Predicting miR-31-5p Targets in Humans
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For miR-31-5p target prediction, the 3' UTR sequences of 17,330 human protein-coding genes were retrieved from the UCSC genome database (https://genome-asia.ucsc.edu/index.html ), and the sequence of mature hsa-miR-31-5p was downloaded from miRBase database (http://www.mirbase.org/ ). Target prediction and context score analyses were performed using the targetscan_50.pl and targetscan_50_context_scores.pl Perl scripts were downloaded from the TargetScan website (http://www.targetscan.org/vert_50/ ). A sum context score of <0.2 was used to filter for the highly probable targets. Consequently, a total of 1,213 putative targets (irrespective of species conservation) were recovered. These targets were further subjected to pathway enrichment analysis using online DAVID functional annotation tools (https://david.ncifcrf.gov ) and GeneGo MetaCore software (Thomson Reuters; New York, NY, USA).
6
Integrative Analysis of Biological Processes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Gene set enrichment analysis was performed using GeneGO Metacore software (Thomson Reuters) to access GO Biological Processes represented in gene expression signatures, produced either from data mining or our RNA-Seq analysis. Gene-biological process functional integration networks were constructed using the Cytoscape 3.2 software with the ClueGO functional analysis plug-in (v 2.2.6)20 (link). Venn diagram analysis was used to identify the intersections of gene signatures from multiple studies, using the Bioinformatics & Evolutionary Genomics Venn diagram tool (VIB/UGent, Belgium). Heatmap generation and hierarchical clustering were done using the “gplots” package in R. Statistical tests utilized in different experiments are identified in the captions of corresponding figures and tables. All graphs and statistical analyses were carried out in GraphPad Prism (Graphpad) and Systat 13 (Systat Software, Inc.). Flow cytometry graphs were generated using FlowJo (Treestar). Principal components analysis was performed using the multivariate statistical analysis software PAST, Version 3.0.
7
Vestitol and Neovestitol Treatment of HeLa Cells
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!