establishing a drug-component-disease-target network, go and kegg enrichment, and geo gene chip dataset analysis in anus eczema

Network Pharmacology and GEO Dataset Analysis of SDG in Anus Eczema Treatment

Anal eczema is an allergic skin condition that affects the perianal region and mucosa, exhibiting various clinical manifestations1. The characteristic symptoms include anal erythema, papules, blisters, erosion, exudates, and crusting. These symptoms mostly arise due to scratching, thickening, and roughness of the affected area2.
Anal eczema, characterized by a prolonged duration of the disease, recurrent attacks, and challenging treatment, can have adverse effects on patients&#39; physical and mental health3. The pathogenesis of anal eczema is not yet clear, and modern medicine suggests that it may be related to local anal lesions, diet, environment, genetics, and other factors4. In addition to avoiding contact with irritants and potential allergens, the treatment of anal eczema mainly focuses on methods such as inhibiting inflammation, anti-allergy, and relieving itching5.
SDG has been extensively utilized for the treatment of anal eczema and other anal conditions. SDG regulates anal skin exudation, reduces moisture, repairs anal skin, and effectively addresses pruritus6,7,8. Furthermore, SDG has the potential to regulate perianus microbiota, thereby improving anus eczema9,10.
Network pharmacology, a novel and interdisciplinary, cutting-edge bioinformatic approach in the realm of artificial intelligence and big data, provides an in-depth exploration of traditional Chinese medicine. This discipline emphasizes the systemic expounding of molecular correlation rules between drugs and diseases from an ecological network perspective. It has been extensively adopted for various aspects, including identifying key active ingredients in herb extracts, deciphering their global mechanisms of action, formulating drug combinations, and studying prescription compatibility. Traditional Chinese prescriptions exhibit the attributes of multi-component and multi-target, signifying their substantial adaptability to the realm of network pharmacology. Driven by this methodology, fresh perspectives have emerged in the examination of complex traditional Chinese medicine systems, furnishing robust technical support for clinical application rationalization and drug innovation11,12,13,14.
This study aims to explore the mechanism of effectiveness of SDG in the treatment of anal eczema. This investigative effort sought to elucidate the mechanism of topical drug administration using a synergistic integration of network pharmacology and GEO datasets. The findings provide valuable insights into the efficacy and underlying mechanisms of SDG in the management of anus eczema, indicating its potential as an effective therapeutic approach for this condition.The detailed workflow diagram of the study is presented in Figure 1.

Author Spotlight: Exploring ShiDuGao's Multi-Target Approach in Anus Eczema Treatment

The Efficacy and Underlying Pathway Mechanisms of ShiDuGao Treatment for Anus Eczema Based on GEO Datasets and Network Pharmacology

1 This article evaluated the feasibility, target<v>2 and the mechanism of ShiDuGao in treating anus eczema. 3 Network pharmacology and GEO database analysis 4 confirms the multi-target nature of SDG 5 in treating anal eczema, 6 specifically by modulating TNF and APK 14, 7 and the CASP3, 8 which are crucial hub targets in the TNF 9 and MAPK signaling pathways. 10 These fundings provide a clear direction 11 for further investigation into SDG's 12 therapeutic mechanism for anal eczema, 13 while highlighting its potential 14 as an effective treatment approach 15 for this debilitating condition.16 Mechanism research is acknowledged<v>17 as the most intricate aspect 18 of herbal prescription investigation. 19 Network pharmacology currently permits diverse aspect 20 of the pharmacentrical field, 21 making a paradigm shift from conventional 22 to contemporary biomedicine, 23 and refining traditional Chinese medicine development. 24 This research combined network pharmacology 25 with GEO dataset to discern to topical drug mechanisms.26 In this study, the pure data generation method<v>27 was used to maximize data utilization 28 by combining modified disease, 29 especially for some diseases that are difficult 30 to build animal models for. 31 The online data are used primarily to predict 32 and verify diseases and drug targets, 33 so as to gather research direction 34 and lay a good foundation 35 for subsequent experimental verification.

Establishing a Drug-Component-Disease-Target Network, GO and KEGG Enrichment, and GEO Gene Chip Dataset Analysis in Anus Eczema

1 To begin, launch the Cytoscape 3.9.1 software<v>2 on the desktop and import the tsv file 3 containing core proteins of anus eczema. 4 Click on the style bar in the control panel 5 to optimize the color, font, and size of the network nodes. 6 For network topology analysis, 7 employ the analyze network function.8 To obtain hub genes, use CytoHubba 9 and establish the drug component disease target network. 10 Open the Metascape website. 11 Select a file or paste a gene list into the dialog box 12 and click the submit button.13 Then select H.sapiens in both input as species 14 and analysis as species, 15 and enable the custom analysis function. 16 In the enrichment option, 17 select GO molecular functions, GO biological processes, 18 GO cellular components, and the KEGG Pathway database. 19 Check pick selective GO clusters, 20 and click on the enrichment analysis button.21 Upon completion of the progress bar, 22 initiate an analysis report page and click 23 to retrieve the enrichment results. 24 Open the GEO2R tool to search 25 and analyze the GEO gene chip database. 26 Open the GEO database website.27 Then enter the keyword or GEO accession 28 and click on the search button. 29 Select the best matching result, 30 and find the reference series. 31 Now on the GEO2R tool website, 32 enter the reference series in the GEO accession box 33 and click the set button.34 Select atopic dermatitis as the experimental group 35 and nonatopic control as the control group. 36 Click the analyze button and wait for the results to appear. 37 KEGG and GO enrichment analyses of 59 key targets 38 identified 218 pathways and over 3, 000 biological processes, 39 highlighting significant pathways in SDG and anal eczema.40 GO analysis on biological processes, cell composition, 41 and molecular function 42 emphasized common targets in SDG and anal eczema. 43 Relevant biological functions included peptidyl-tyrosine 44 phosphorylation and regulation of cell-cell adhesion.

establishing-drug-component-disease-target-network-go-kegg-enrichment

Research

JoVE Journal

Medicine

Anus eczema is a chronic and recurrent inflammatory skin disease affecting the area around the anus. While the lesions primarily occur in the anal and perianal skin, they can also extend to the perineum or genitalia. ShiDuGao (SDG) has been found to possess significant reparative properties against anal pruritus, exudation control, moisture reduction, and skin repair. However, the genetic targets and pharmacological mechanisms of SDG on anal eczema have yet to be comprehensively elucidated and discussed. Consequently, this study employed a network pharmacological approach and utilized gene expression omnibus (GEO) datasets to investigate gene targets. Additionally, a protein-protein interaction network (PPI) was established, resulting in the identification of 149 targets, of which 59 were deemed hub genes, within the "drug-target-disease" interaction network.
The gene function of SDG in the treatment of perianal eczema was assessed through the utilization of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis. Subsequently, the anti-perianal eczema function and potential pathway of SDG, as identified in network pharmacological analysis, were validated using molecular docking methodology. The biological processes associated with SDG-targeted genes and proteins in the treatment of anus eczema primarily encompass cytokine-mediated responses, inflammatory responses, and responses to lipopolysaccharide, among others. The results of the pathway enrichment and functional annotation analyses suggest that SDG plays a crucial role in preventing and managing anal eczema by regulating the Shigellosis and herpes simplex virus 1 infection pathways. Network pharmacology and GEO database analysis confirms the multi-target nature of SDG in treating anal eczema, specifically by modulating TNF, MAPK14, and CASP3, which are crucial hub targets in the TNF and MAPK signaling pathways. These findings provide a clear direction for further investigation into SDG's therapeutic mechanism for anal eczema while highlighting its potential as an effective treatment approach for this debilitating condition.

This investigative effort sought to elucidate the mechanism of topical drug administration using a synergistic integration of network pharmacology and gene expression omnibus (GEO) datasets. This article evaluated the feasibility, target, and mechanism of ShiDuGao (SDG) in treating anus eczema.

Anus eczema is a chronic and recurrent inflammatory skin disease affecting the area around the anus. While the lesions primarily occur in the anal and ...

Identifying Disease Targets and Active Components in Traditional Chinese Medicine for Anus Eczema

Predicting the Binding of SDG Active Components to Anus Eczema Targets

1 To begin, 2 open the traditional Chinese Medicine Systems 3 Pharmacology database. 4 Using the chemical name search box, 5 search the selected ingredient names 6 to download the corresponding 3D structure files 7 in Mol2 format. 8 To download the crystal structures of the key targets, 9 open the RCSB Protein database.10 In the search box, 11 search the target names 12 and download the corresponding 13 crystal structure files in PDB format. 14 Import ingredients and target structure files 15 in the analysis software. 16 Click Edit, then Delete Water to delete water molecules.17 To add hydrogens, click on Edit, Hydrogens, and Add. 18 Set the ingredients as the ligand. 19 Select whole targets as the receptor 20 and perform blind docking.21 To determine the range of molecular docking, 22 select the receptor and ligand in sequence. 23 Click on Grid, then Grid Box to adjust the grid box 24 to include the entire model. 25 Click on File and Close to save the current grid box status 26 and save the files in GPF format.27 Now click on Run and Run Auto Grid Four, 28 click Parameter File Name, and Browse, 29 to select the GFP file. 30 Then click the Launch button. 31 For molecular docking, 32 open the auto doc four and click on docking, Macromolecule, 33 and set rigid file name to select the receptor.34 Then click on Docking, Ligand and open, 35 or choose to select the ligand. 36 Now click on Docking 37 and Search Parameters to set operation algorithms. 38 Then click Docking and Docking Parameters 39 to set docking parameters.40 Select the DPF file and click the launch button. 41 Save files in the DPF format. 42 Click on Analyze, Docking, 43 and open to select the DLG file.44 Then click on Analyze and Macromolecule 45 to open the receptor. 46 Now click on Analyze, Confirmations, and Play, 47 ranked by energy to analyze the results. 48 Finally, click Set Play, 49 and write complex to save the results in PDBQT format.50 Import the docking files into PyMOLE, 51 then select the ligand and click on Action, Find, 52 Polar Contracts and to other atoms and object 53 to display hydrogen bonds between ligands 54 and the external environment. 55 Click on single letter C to change color. 56 Click Action and Extract Object.57 Click Show, then Sticks, 58 to show the stick structure of the receptor, 59 identify the residuals connected to ligands 60 and show the stick structure. 61 Then click Wizard and Measurement 62 and click on two atoms in sequence. 63 Click Label then Residue to show the label of the residues.64 If necessary, adjust the background color and transparency. 65 Finally, click File, then Export Image As 66 to save the picture. 67 In the atopic dermatitis group, 68 GEO database analysis revealed upregulation 69 of P-P-A-R-G, E-G-F-R, T-N-F 70 and P-T-P-R-C MMP Nine, MAPK 14, 71 and CASP Three were downregulated.72 Docking analysis confirmed the interaction 73 between active SDG components 74 and potential target proteins 75 indicating their significant role in anal eczema treatment. 76 Indigo and Berberrubine demonstrated strong binding activity 77 with energy's less than minus five kilo calories per MOL, 78 emphasizing their therapeutic potential.