StemChecker: a web-based tool to discover and explore stemness signatures in gene sets

Nucleic Acids Research, 2015 · DOI: 10.1093/nar/gkv529 · Published: May 24, 2015

Simple Explanation

Stem cells offer regenerative abilities, holding potential for treating diseases like diabetes and heart disease. Identifying 'stemness signatures' is key to understanding stem cells, but using them is hard due to lack of resources. StemChecker is a new tool for stemness analysis, based on a collection of stemness signatures. It lets researchers find stemness signatures in gene sets, avoiding extensive literature research and data processing. StemChecker presents results graphically and statistically, helping to reveal regulatory programs and stemness-associated processes in diseases like cancer. It expands the online tools available for stem cell biology and disease research.

Study Duration

Not specified

Participants

Not specified

Evidence Level

Not specified

Key Findings

1
StemChecker is based on the most extensive and up-to-date curation of published stemness signatures.
2
The data integration in StemChecker can help to identify subsets of genes whose association with stemness is supported by multiple independent evidence.
3
StemChecker combines and integrates these data, providing an easy-to-use interface, which displays the overall results in an intuitive and meaningful way, while still providing a detailed individual gene analysis, together with the statistical significance of the overlap.

Research Summary

StemChecker is a web-based tool designed to help researchers discover and explore stemness signatures in gene sets. It addresses the limitations of existing resources by providing a comprehensive and easy-to-use platform. The tool is based on a curated collection of stemness signatures and transcription factor target gene sets. It allows users to input their gene sets and identify overlaps with known stemness signatures and regulatory programs. StemChecker offers an intuitive graphical display and detailed statistical results, enabling researchers to gain insights into stemness-associated processes and regulatory mechanisms in various biological contexts, including diseases like cancer.

Practical Implications

Accelerated Stem Cell Research

StemChecker streamlines the process of identifying stemness signatures, allowing researchers to quickly assess the potential involvement of stem cell-related mechanisms in their studies.

Improved Understanding of Regulatory Programs

By integrating transcription factor target gene sets, StemChecker helps to elucidate the regulatory programs underlying stem cell identity and differentiation.

Enhanced Disease Research

The tool facilitates the investigation of stemness-associated processes in diseases like cancer, potentially leading to new therapeutic strategies.

Study Limitations

1
The signatures can be substantially distinct, particularly the ones derived by different experimental approaches, making the analysis and comparison between signature gene sets a non-trivial task
2
Although no ‘universal’ stemness signature has been established
3
Currently, StemChecker relies on manually curated data, which may be subject to biases or omissions.

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