• 12.1 analysis of language differences and geo code sets Data download and sorting


    1、 Example introduction In this section, Download gse1009 data set and use limma package for difference analysis. GSE1009   Sample size:There were 6 samples in total, of which 3 were glomerular samples of diabetes nephropathy (DN) and the other 3 were normal glomerular samples. Use chip:Affymetrix Human Genome U95 Version 2 Array。 Platform:GPL8300。 2、 Examples of […]

  • “Pit” of gse53625


    Students and teachers who study esophageal cancer must know that gse53625 data set comes from《LncRNA profile study reveals a three-lncRNA signature associated with the survival of esophageal squamous cell carcinoma patients》This article. As far as I know, this should be the largest data set of esophageal squamous cell carcinoma at present, and the classification is […]

  • [block] cibersort R calculated the infiltration fraction of 22 immune cells


    Comprehensive developepper authors’ articles and their own operations are summarized as follows for later use.If you have any questions, welcome to communicate Robust enumeration of cell subsets from tissue expression profiles | Nature MethodsThe above is an article by cibersortThree files are required to use the cibersort tool: 1、Cibersort.R 2、LM22.txt 3、genes_exp.txt 1、Cibersort.R This file is […]

  • Psrobot usage process | wheat


    ⭐⭐⭐ This article records my psrobot using psrobot_ Tar module is the process of identifying target genes. Stepped on many pits for the younger brothers and sisters in the laboratory to learn from. Reference: PsRobot: a web-based plant small RNA meta-analysis toolbox MiRNA target gene prediction: psrobot psRobot_tarModule is designed to find potential small RNA […]

  • How to map metabolic pathways with genome?


    Only the genome. I wanted to draw a metabolic map. I tossed about it for several days. Finally, I found that it was the fastest to look at the official website documents carefully. There were few detailed explanations found on the website. Most of them only talked about one part, so it was the fastest […]

  • Haven’t you done the m6A related research on the fire?


    m6A regulator-based methylation modification patterns characterized by distinct tumor microenvironment immune profiles in colon cancer Based on the methylation modification mode of m6A regulator, it shows different immune characteristics of tumor microenvironment in colon cancer Published journal: theranostics Date of publication: 2021 Jan 1 Impact factor: 8.579 DOI:  10.7150/thno.52717 1、 Research background The methylation of N6 […]

  • Can Cerna pure student letters still be sent for 5 points now? Come and watch


    Title: comprehensive analysis of Cerna network to explore the prognostic characteristics of renal papillary cell carcinoma (kirp) The idea of establishing a disease-related Cerna network is roughly as follows: first screen the lncrna (circrna), miRNA and mRNA that are significantly differentially expressed in the disease, and then predict the interaction between them, so as to […]

  • 2021-07-28 logfc interpretation of limma package difference analysis results


    First of all, we should understand that the input parameter accepted by limma is an expression matrix, and it is the expression matrix after log (with 2 as the bottom). Then, the value of the last calculated logfc column is actually the value of the average expression of case group minus the average expression of […]

  • Qingqi SCI: 12 Redox related gene + ccrcc (5 + points)


    PMID:33425212Published magazine:Oxidative Medicine and Cellular Longevity Knowledge points Redox: redox reaction, which plays a significant role in the progression of tumor. The redox related pathway shown by the authors in GSEA was foundGO_CELL_REDOX_HOMEOSTASISandGO_RESPONSE_TO_REDOX_STATE, there are two redox related gene sets. Redox related lncrnas: redox related lncrnas. Setting criteria:Pearson Correlation Test, |Cor| > 0.5 and p.adj […]

  • Reasonable range of CT value in qPCR experiment


    What is the CT value?What is the effect of CT value?What is the normal range of CT value?Why is the CT value too large or too small? (the content of this article is extracted from the Internet, invaded and deleted!) CT value is fluorescence quantificationPCRThe most important result presentation form. It is used for calculationgeneExpression […]

  • Analysis on the inference of gene regulation network of genie3


    GENIE3 GENIE3(GEne Network Inference with Ensemble of trees) , a tree based ensemble learning algorithm is used to infer gene regulatory networks from gene expression data. Tips: at the end of genie33Not the third version of genie, but because it is pronounced through a French accent,treeandthreeThe pronunciation is the same. Attach two French sounds:tree, three […]

  • Precautions for ciberport when quantifying immune infiltration


    Precautions for ciberport We have given several examples of the use of ciberport, but there are still some questions. As long as there are questions, I feel uneasy.For example:1. What kind of data does ciberport need?Is it chip data or sequencing data? What format is it? Do you need to take log?2. What does the […]