Bioinformatics Analysis FAQ

• • How to Perform Pathway Analysis Using the KEGG Database

  When performing pathway analysis, the KEGG (Kyoto Encyclopedia of Genes and Genomes) database is a very useful tool. KEGG provides rich bioinformatics resources, including annotations and classifications of genes, proteins, metabolites, and detailed descriptions and diagrams of various biological pathways. Below are the detailed steps for using the KEGG database for pathway analysis:

• • How to Perform PLS-DA Analysis Using SIMCA-P

  The SIMCA-P software is capable of creating and interpreting PLS-DA models, though the specific steps may differ depending on the version of SIMCA-P being used. The general procedure is outlined as follows: Launching SIMCA-P and Creating a New Project: Open the SIMCA-P software. Select "New Project" and assign a name to the project. Importing Data: Within the project, select "Import Data". Import the data from your source (e.g., an Excel file). Ensure that the data is formatted appropriately, including.....

• • What Are the Differences Between Principal Component Analysis and Cluster Analysis, and When Should Each Method Be Used

  Differences Between Principal Component Analysis (PCA) and Cluster Analysis: 1. Different Objectives: (1) The objective of PCA is to transform the original data into a set of new variables, called principal components, through a linear transformation to reduce the dimensionality of the data while retaining as much information as possible. (2) The objective of cluster analysis is to partition data samples into different groups so that the similarity of samples within the same group is high, while the........

• • RNA-Seq Experimental Workflow

  RNA-Seq is a technique that utilizes high-throughput sequencing to investigate the presence and quantification of RNA in cells. The following outlines the standard workflow of an RNA-Seq experiment: 1. Sample Preparation: Begin by collecting the cellular or tissue samples pertinent to your study. 2. RNA Extraction: Employ an appropriate method, such as column-based or bead-based technology, to extract total RNA from these samples.

• • How Can KEGG Analysis Results Be Visualized?

  When performing analyses using KEGG (Kyoto Encyclopedia of Genes and Genomes), a variety of tools and approaches are available for effective visualization of the results:   KEGG Mapper KEGG Mapper is a web-based tool that enables the visualization of KEGG annotations, such as genes, metabolites, or other biological entities, within the context of KEGG pathway diagrams. Users can input data such as gene expression levels or metabolite concentrations and select appropriate analysis modes, including enri......

• • Why Do KEGG Results Show Diseases Instead of Pathways?

  The display of disease entries rather than pathways in KEGG search results could be due to several reasons. Reassessing the following factors may help resolve the issue:   Search Keywords If the input keywords predominantly contain genes or proteins associated with diseases, KEGG analysis is more likely to match these terms to disease-related pathways and entries. For example, if the dataset originates from tumor samples, the genes involved are more often linked to cancer-related pathways.   Database ......

• • How to Correctly Interpret Principal Components After Conducting Principal Component Analysis (PCA)?

  After performing Principal Component Analysis (PCA), a set of principal components is obtained, with each component being a linear combination of the original variables. Interpreting the principal components can be approached from several perspectives:   Understanding the Meaning of Principal Components Principal components are linear combinations of the original variables, arranged such that the first principal component explains the greatest variance in the data, the second principal component expla......

• • How Can PLS-DA (Partial Least Squares Discriminant Analysis) Be Used to Select Diagnostic Cytokines?

  Partial Least Squares Discriminant Analysis (PLS-DA) is a statistical method used for selecting and identifying biomarkers with diagnostic value, such as cytokines. When using PLS-DA for diagnostic screening of cytokines, the following steps are generally followed:   Data Collection and Preprocessing First, collect datasets containing the levels of the target cytokines, which are typically derived from biological samples such as blood or tissue samples. Next, preprocess the data by standardizing it, h......

• • How Can GO and KEGG Analysis Be Performed with Only the Amino Acid Sequence?

  If you only have the amino acid sequence of a protein, performing GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis involves aligning your sequence with known genes or proteins and using this information for functional annotation and pathway analysis. The detailed steps are as follows:   Sequence Alignment and Protein Identification Use BLAST (Basic Local Alignment Search Tool) or other sequence alignment tools to compare your amino acid sequence with known proteins in pub......

• • What Do the Axes, Black Circles, and Red Bars Represent in GO Functional Annotation Analysis Plots?

  GO functional annotation analysis plots are commonly used bioinformatics tools for annotating and analyzing the functions of genes or proteins.   What Do the Axes Represent? 1. X-axis The X-axis typically represents different GO functional terms or categories. GO (Gene Ontology) is a standardized classification system used to describe the functions of genes and proteins, encompassing three main aspects: Molecular Function, Cellular Component, and Biological Process. Each point on the X-axis correspond......