3.Bioinfo Basics

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Objective: Prepare bioinformatics basic knowledges especially expression data

Time estimated: 5 h; taken 6 h;

Date started: 2023-1-12 ; completed: 2023-1-20

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Abstractions for Bioinformatics

• Notes: "Abstractions" for Bioinformatics

Storing Data

• Notes: construction principles for large, multi-user, scalable database systems

The NCBI Database and Services

• See notes for MGY441

Miscellaneous Databases for Bioinformatics

• **SGD:** Check available info of mbp1 on

  1. Analyze → Gene Lists page

     • Get list of 29 genes: https://yeastmine.yeastgenome.org/yeastmine/bagDetails.do?bagName=Gene+list+for+S.+cerevisiae+31+Jan+2023+2.14&trackExecution=false
     • Find common: all ORF class

  2. Analyze → GO Slim mapper page

  • "Yeast GO-Slim: Function" as the ontology of terms, then "SELECT ALL Terms...”
  1. Repeat for for "GO-Slim:Process”
  2. read results in R with read.file()

• STRING database: functional interactions

  1. search for saccharomyces cerevisiae Mbp1 interactors
  2. add proteins with “+”

Data Integration

• Notes: concepts and approaches to data integration in bioinformatics

• Use UniProt ID mapping service, mapping NP_010227 to P39678.

  Issue: 404 Solution: search for mapping manually

Expression Analysis

• Notes: measuring and analysing gene expression levels
  • Normaliza counts: RPKM or FPKM(probabilistic, fold- changes)
  • Raw counts(edgeR)

Discovering Differentially Expressed Genes

• Notes: discovering differentially expressed genes in high-throughput data
  • M/A plot:
    • y: log(sample) – log(control),
    • x: avg, the mean of sample and control
• GEO2R
  1. Query on GEO
  2. Link to reference series
  3. GEO2R(GEO2R video tutorial)

     • No error distn, but now

       

Multiple Testing and Significance

• Notes: multiple testing

💡 **Conclusion and outlook**: Went through the preparation unit.