TransPilot (v1.0)

Testing the significance of ranked TF-target sets in genome-wide transcriptome profiling data using weighted rank correlation statistics.

Downloads Project Source Tutorials

1. Select TF-target set

Select a genome using the select boxes on the right. By default, the first 15 genomes are listed. Type the scientific name of the organism in the search box to filter the results.

Homo sapiens is a species of primate in the family Hominidae (great apes).

Taxonomy ID: 9606

Common name: Human

Number of GSETs: not defined

Select a Genome

HOCOMOCO Jaspar

2. Upload DEG list

We provide the RANKED DEG list in TAB-delimited text file format.

The RANKED DEG list file format is specified as one gene per line. The first column contains the official gene symbol, and the second column contains the RANK value, which can represent the extent of differential expression. Columns are separated by TAB characters.

The RANKED DEG list file can be generated by our gene list creation tool, GENE_Spark, using your transcriptome profiling data.

8 CPU threads

16 CPU threads

TransPilot Server Accumulated Successful Runs.

We provide correlation plots to illustrate the relationship between a TF-target set and a DEG list.

The upper plot illustrates genes that have transcription factor binding sites. The lower plot illustrates genes that do not have transcription factor binding sites. The X-axis represents the rank values of the extent of differential expression. Bar height is a quantitative metric representing the potential of binding with the transcription factor. Edge genes (bars) can be highlighted in green. The red vertical line represents the weighted average of the extent of differential expression values.

We provide GSEA dot plots to illustrate the enrichment analysis of transcription factor target genes.

The top portion of the plot shows the running enrichment score (ES) for the gene set as the analysis walks down the ranked list of genes. The peak of the curve—the highest positive or negative point—represents the enrichment score (ES), which reflects how overrepresented the gene set is at the top or bottom of the ranked list. The middle portion indicates how the genes in the dataset are ranked (e.g., based on fold change or correlation with phenotype). The bottom portion shows where the genes from the gene set appear along the ranked list.

Target gene network regulated by key transcription factors.

The network can be exported to a file and imported into the Cytoscape software package for visualization.

Publications

Grit paper

Tinghua Huang, Hong Xiao, Qi Tian, Zhen He, Min Yao. Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics. PloS Computational Biology, 2022.
Flaver paper

Min Yao, Hao He, Binyu Wang, Xinmiao Huang, Sunli Zheng, Jianwu Wang, Xuejun Gao, Tinghua Huang. Testing the significance of ranked gene-sets in genome-wide transcriptome profiling data using weighted rank correlation statistics, Current Genomics, 2024.
Huang Tinghua, Niu Siqi, Zhang Fanghong, Wang Binyu, Wang Jianwu, Liu Guoping, Yao Min, Correlating gene expression levels with transcription factor binding sites facilitates identification of key transcription factors from transcriptome data, Frontiers in Genetics, 2024.

FAQs

Some of the species are not available?

The species in the list marked as 'coming soon...' will be updated when the analysis is finished.
What are the differences between TF-target sets?

The JASPAR and HOCOMOCO options are for TF-target subsets built based on PWMs deposited in the JASPAR and HOCOMOCO databases, respectively. Based on the TFBSs predicted by the ANN model, three TF-target sets were constructed, with the ranking scores defined as follows: ANN score (ANN set), sign(correlation coefficient) X ANN score (Dir set), and correlation coefficient (CRank set).
The downloading process of the TF-target dataset was taken over by a downloader software such as XunLei?

You have to uninstall XunLei or disable such features.
Something doesn't work. Can you fix it?

Yes! Please report all issues to the maintainer: Dr. Tinghua Huang and Dr. Min Yao.
What browsers are supported?

All modern desktop browsers are supported (Firefox, Chrome, Safari and IE9).

Maintainer

Dr. Tinghua Huang, Yangtze University, Email: thua45@yangtzeu.edu.cn
Dr. Min Yao, Yangtze University, Email: minyao@yangtzeu.edu.cn

TransPilot (v1.0)

1. Select TF-target set

2. Upload DEG list

3. Results

4. Correlation Graph

5. Annotation

6. Plot Enrichment Graph

7. Build Network

Publications

Grit paper

Flaver paper

FAQs

Some of the species are not available?

What are the differences between TF-target sets?

The downloading process of the TF-target dataset was taken over by a downloader software such as XunLei?

Something doesn't work. Can you fix it?

What browsers are supported?

Maintainer