Hello Dr.Asif's i have some chemical compounds from herbal and produc polyherbal. i want to find out the general function using erichment KEGG pathways and heatmap. How to convert the chemical compound to get hetapmap or KEGG ? can u help me step by step ?
To find the functions of your chemical compounds and visualize their KEGG pathway enrichment using a heatmap. Step 1: Get Standard Identifiers for Your Compounds If your compounds are listed by common names, first convert them to standardized identifiers that KEGG recognizes, such as KEGG Compound IDs (CIDs), PubChem IDs, or ChEBI IDs. Here’s how: 1. PubChem: Go to the PubChem website, search each compound, and retrieve its PubChem ID or other identifiers. 2. KEGG COMPOUND Database: Visit the KEGG Compound Database to check if KEGG already has IDs for your compounds. If you find KEGG CIDs, these can be used directly for pathway mapping. Step 2: Map Compounds to KEGG Pathways Once you have KEGG CIDs, you can identify which pathways are related to your compounds using the KEGG Mapper tool. Here’s how: 1. Go to KEGG Mapper on the KEGG website. 2. Select the Search Pathway option. 3. Enter the KEGG CIDs for your compounds in the search field. 4. KEGG Mapper will display pathways that include your compounds, highlighting the specific pathways they are involved in. This step helps you determine which biological pathways are influenced by the compounds you’re studying. Step 3: Perform KEGG Pathway Enrichment Analysis To understand the broader functions of your compounds, pathway enrichment analysis can identify which pathways are statistically enriched with your compounds compared to random chance. Some ways to do this: • Online Tool: Use a web-based tool like MetaboAnalyst, which supports pathway enrichment. Upload your list of KEGG CIDs or PubChem IDs, select the enrichment analysis option, and choose KEGG as the pathway database. • Results: The tool will provide a list of pathways that are significantly enriched, often ranked by p-value or enrichment score. This will give you a clearer view of which biological functions or processes are linked to your compound set. Step 4: Create a Heatmap for Visualization To visualize the enriched pathways in a heatmap: 1. Pathway Scores: Collect the enrichment scores or p-values from the enriched pathways identified in Step 3. 2. Heatmap Tool: Use a tool like Excel or MetaboAnalyst, where you can create a heatmap. In MetaboAnalyst, you can input the enrichment data, and the platform has a heatmap function that organizes pathways by similarity, making it easier to see patterns in enrichment. The heatmap will show the intensity or significance of enrichment for each pathway, making it easy to identify which pathways are most influenced by your compounds. Following these steps, you’ll be able to map your compounds to pathways, perform enrichment analysis, and visualize the results with a heatmap.
![[LIVE] : ONE ลุมพินี 91 | คู่เอก "คมอาวุธ vs อเล็กเซย์"](http://i.ytimg.com/vi/V0RkEfYFsgM/mqdefault.jpg)
Excellent website, thanks
Glad you like it
I will do this for MIC and BMD
Sure
Provide more such videos like related to Transcriptome and metabolics
Transcriptomic | RNA seq data Interpretation | DEGs | GO | KEGG
th-cam.com/video/xc2zEI_5pmw/w-d-xo.html
A bioinformatics guide to Metabolomic Data analysis interpretation
th-cam.com/video/K2qYuL3l0C4/w-d-xo.html
Videos are already uploaded 👆
Okay thankyou sir
Thankyou so much sir
Glad you like it
Hello Dr.Asif's i have some chemical compounds from herbal and produc polyherbal. i want to find out the general function using erichment KEGG pathways and heatmap. How to convert the chemical compound to get hetapmap or KEGG ? can u help me step by step ?
To find the functions of your chemical compounds and visualize their KEGG pathway enrichment using a heatmap.
Step 1: Get Standard Identifiers for Your Compounds
If your compounds are listed by common names, first convert them to standardized identifiers that KEGG recognizes, such as KEGG Compound IDs (CIDs), PubChem IDs, or ChEBI IDs. Here’s how:
1. PubChem: Go to the PubChem website, search each compound, and retrieve its PubChem ID or other identifiers.
2. KEGG COMPOUND Database: Visit the KEGG Compound Database to check if KEGG already has IDs for your compounds.
If you find KEGG CIDs, these can be used directly for pathway mapping.
Step 2: Map Compounds to KEGG Pathways
Once you have KEGG CIDs, you can identify which pathways are related to your compounds using the KEGG Mapper tool. Here’s how:
1. Go to KEGG Mapper on the KEGG website.
2. Select the Search Pathway option.
3. Enter the KEGG CIDs for your compounds in the search field.
4. KEGG Mapper will display pathways that include your compounds, highlighting the specific pathways they are involved in.
This step helps you determine which biological pathways are influenced by the compounds you’re studying.
Step 3: Perform KEGG Pathway Enrichment Analysis
To understand the broader functions of your compounds, pathway enrichment analysis can identify which pathways are statistically enriched with your compounds compared to random chance. Some ways to do this:
• Online Tool: Use a web-based tool like MetaboAnalyst, which supports pathway enrichment. Upload your list of KEGG CIDs or PubChem IDs, select the enrichment analysis option, and choose KEGG as the pathway database.
• Results: The tool will provide a list of pathways that are significantly enriched, often ranked by p-value or enrichment score.
This will give you a clearer view of which biological functions or processes are linked to your compound set.
Step 4: Create a Heatmap for Visualization
To visualize the enriched pathways in a heatmap:
1. Pathway Scores: Collect the enrichment scores or p-values from the enriched pathways identified in Step 3.
2. Heatmap Tool: Use a tool like Excel or MetaboAnalyst, where you can create a heatmap. In MetaboAnalyst, you can input the enrichment data, and the platform has a heatmap function that organizes pathways by similarity, making it easier to see patterns in enrichment.
The heatmap will show the intensity or significance of enrichment for each pathway, making it easy to identify which pathways are most influenced by your compounds.
Following these steps, you’ll be able to map your compounds to pathways, perform enrichment analysis, and visualize the results with a heatmap.
Subperb
Glad you like it