TransPilot (v1.0)

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

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1. Select Gene-set

Select a Genome using the select boxes in the right, the default listed the first 15 genomes, typing the scientific name of the orgnisms in the search box to filter 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 Gene-list

We provide TAB text file formats for RANKed gene list.

The RANKed gene list file format is specified by one gene per line, the first column is the official gene syombl, the second column is the RANK value, the RANK value can be the extent of differential expression. Each column was seprated by a TAB character.

The RANKed gene list file can be produced by out gene list creation tool (GENE_Spark), using your gene transcriptome profiling data.

8 CPU threads

16 CPU threads

Flaver Server Accumulated Successful Runs.

We provide correlation plots for the illustration of the relationship between gene-set and gene-list.

The upper plot illustrated the genes have transcription factor binding site. The lower plot illustrated the genes have no transcription factor binding site. The X axis represented the rank values of the extent of deferential expression. Bar height is a quantitative metric representing the potential of binding with the transcription factor. Edge genes (Bars) can be highlighted with green colors. The red vertical line represent the weighted average of the extent of deferential expression values.

We provide GSEA dot plots for the illustration of the enrichment analysis of the target genes for the transcription factors.

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 (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 gene list. The middle part of the plot shows how genes in the dataset are ranked (e.g., based on fold change or correlation with phenotype). The bottom part of the plot indicates where the genes from the gene set appear in the ranked list.

The network of the target genes regulated by the key transcription factors.

The network can be exported to file and imported into Cytoscape software package for graphing.

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 "comming soon..." will be updated when the analysis is finished.
What are the differences between GSETs?

The JASPR and HCOMOCO options are for TF-target subsets build based on PWMs deposited in JASPR and HCOMOCO database, respectively.
The download of the TF-target dataset was taken over by a downloader software like 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 Gene-set

2. Upload Gene-list

3. Results

4. Plot 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 GSETs?

The download of the TF-target dataset was taken over by a downloader software like XunLei?

Something doesn't work. Can you fix it?

What browsers are supported?

Maintainer