Bioinformatics Analysis FAQ
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• 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 ......
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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......
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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......
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• 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......
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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......
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• How to Analyze KEGG Pathways of Differential Metabolites?
To analyze the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways of differential metabolites, the following steps can be followed: Data Collection First, it is essential to collect and prepare data on differentially expressed genes or metabolites. These data are typically obtained from transcriptomic or metabolomic experiments. Data Preprocessing The collected data must undergo necessary preprocessing, such as normalization and the selection of differentially significant metabolites or genes......
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To plot Principal Component Analysis (PCA) and Partial Least Squares (PLS) regression in chemometrics without programming, you can use specialized data analysis software such as Origin or Minitab, which provide intuitive user interfaces and comprehensive graphical options. Below are the basic steps for using these types of software: Plotting PCA and PLS with Origin 1. Data Import (1) Open Origin and create a new project. (2) Import your dataset into the worksheet. 2. Perform PCA Analysis (1) Click......
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The use of protein IDs for GO/KEGG enrichment analysis and the conversion of protein IDs to gene IDs for analysis may produce similar results; however, some differences still exist. UniProt primarily focuses on providing detailed functional, structural, and interaction annotations for individual proteins. In contrast, GO/KEGG enrichment analysis aims to identify biological functions or pathway enrichment patterns within a set of genes or proteins.When investigating the characteristics of a specific ......
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• How to Determine the Quality of Transcriptomic and Genomic Data Obtained from Sequencing?
Evaluating the quality of sequencing data, such as transcriptomic and genomic data, is a critical step in the sequencing workflow. The following strategies and tools are helpful for assessing the quality of sequencing data: Quality Check of Raw Data 1. FastQC This widely used tool provides an overview of the data quality for each sequencing sample. It offers multiple quality metrics, including sequencing quality, sequence length distribution, and the proportion of duplicated sequences. 2. MultiQC ......
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When selecting differential pathways and proteins, both strategies are viable: proteins can be selected based on known pathways, or pathways can be inferred from differentially expressed proteins. Additionally, Gene Ontology (GO) analysis can be employed for functional interpretation. Should Proteins Be Chosen Based on Pathways, or Pathways Based on Proteins 1. Selecting Proteins Based on Pathways If a specific pathway is known to be altered under particular conditions, proteomic analysis can be uti......
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