Tool: website: Express online visualization of human genome pathways
gravatar for serena_yu
2.8 years ago by
serena_yu110 wrote:

Hello everyone,

I developed a bioinformatics tool to visualize human genome pathways.

When I was doing molecular biology research myself, I always had difficulty to get an overview of some genes in the vast human genome network. We often search it through Google image for pathways maps, or search from antibody companies, but these sources of pathways maps are hardly customized for our genes of interest, and was hardly complete for all the pathways the gene of interest leads to. From this point, I developed this website to provide a light-weight, quick tool for researchers to lookup human genome pathways based on their genes of interest.

It involves 2 modules:

Module 1. Single gene pathway analysis:

Given a gene, find the up-stream and/or downstream molecular pathways. You may choose the length of pathways to search for. demo for module 1 I think it is self-explanatory from the first sight on this map. I input Ago2, and got its upstream and downstream genes. You may choose how many genes to search for and how many levels down into the molecular pathway. The search algorithm is based on academic reports: the gene interactions that are reported most will come first.

There is a button below that can generate a list of references from PubMed for all the genes listed. demo for the reference button demo for the reference list



Module 2: Pathway enrichment analysis:

Given a list of genes, find the pathways that connect them. If a gene cannot be connected, it will not be shown in the figure. demo for module 2

For example, if I ran some PCR in my cell model and found TP53, AKT1, and PIK3R3 were the most significant genes, I would want to know what other genes could be involved. In a quick search on this website I would find how these genes are related in the human genome network, and figure out ERBB3, RB1, PTK2, and PIK3CA may be worth for further investigation.

Same as Single gene pathway analysis, there will also be a button appearing below the graph, which will generate a list of references for you:

demo for references in module 2

You must have noticed that some genes are reported repeatedly, so they can generate a long list.



The database of this website currently is based on BioGrid's open dataset for 1 Dec 2017. I will keep updating when I get new data sources. It currently records 16,760 genes and 369,824 papers.


Serena (Feng) Yu, Ph.D.


Sydney, Australia

ADD COMMENTlink modified 2.7 years ago • written 2.8 years ago by serena_yu110
gravatar for Ibrahim Tanyalcin
2.8 years ago by
Ibrahim Tanyalcin1.1k wrote:

It's great work! Given that you have molecular biology backgrounds apparently has given you a lot of intuition about what might be useful for other researchers.

The tool looks clean and nifty. Don't forget that you are developing these tools for a much smaller audience when compared to other areas of programming so keep building on this tool even in case of absence of feedback.

Good luck & congrats

ADD COMMENTlink written 2.8 years ago by Ibrahim Tanyalcin1.1k

I'm glad to hear that. I hope it can help a lot people in their research. I will keep improving it.

Actually, do you know of any gene interaction databases that distinguish between upregulation and downregulation? You must have noticed currently I am drawing everything using arrows, but I expect to show the nature of the interaction.

ADD REPLYlink written 2.8 years ago by serena_yu110

Would string db help?

ADD REPLYlink written 2.8 years ago by Ibrahim Tanyalcin1.1k
gravatar for serena_yu
2.8 years ago by
serena_yu110 wrote:

Update 14 Dec 2017:

Now it supports common synonyms of genes. For example, inputing "JNK" will bring you to MAPK8, which is JNK's official symbol.

All the gene names on the reference list are now hyper-linked to its page on Entrenz Gene.

ADD COMMENTlink written 2.8 years ago by serena_yu110
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