What is GLITTER?

GLITTER stands for Gene Link Inspector Through Tissue-specific coExpRession. It is designed to examine the functional relatedness of disease susceptibility genes according to tissue-specific gene expression profiles. GLITTER can also shed light on the specific tissues in which susceptibility genes might exert their functions. The gene expression profiles are the RNA-Seq data (version 6) from the Genotype-Tissue Expression Project (GTEx) for 49 different tissues. The hypothesis behind GLITTER is that susceptibility genes are not random, but tend to be functionally related in specific tissues implicated in diseases.


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What information does GLITTER need?

GLITTER requires four items of information as input:

  1. a list of genes to be examined. The gene names can either be official symbols or ENSEMBLE IDs;
  2. the type of correlation to choose ('Pearson' or 'Biweight');
  3. the cutoff for correlation coefficients that are used to define connections between two genes;
  4. the number of simulations for estimating the statistical significance of the observed number of connected gene pairs among input genes.

What does GLITTER do with the input?

GLITTER quantifies the functional relatedness of susceptibility genes by calculating the total number of connected gene pairs based on gene coexpression patterns. Its statistical significance is estimated by randomly sampled gene sets, while matching for gene numbers, gene sizes and GC content. Random gene sets are generated from the human Gencode v19 gene annotation by default. The users can also choose to generate random gene sets from customized gene sets, such as those represented in a GWAS array.


What does GLITTER provide in the output?

GLITTER returns two sets of results: 1) a summary text file with each line containing meta information for each tissue, including tissue name, total number of expressed genes, the number of input genes expressed, the number of connected gene pairs among input genes, and the p-value assessing the significance of the observed number of connected gene pairs of input genes; and 2) a series of PDF files for the histogram of the number of connected gene pairs from random gene sets for each tissue. The number of connected gene pairs from input genes is also indicated by a virtual red line in the PDF file for each tissue. GLITTER sends an email notice to users once the job is done alerting them that the results are ready to be downloaded from the website.



Updates

2016-11-16

  • GLITTER has been updated to output connected gene pairs among input genes for each tissue.

2016-04-17

  • User specified reference gene list is now allowed as an option to choose background genes for generating random gene sets. The default background gene set is 'gencode.v19' annotated genes.

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Reference

Xiangtao Liu, Pengfei Yu, Chao Cheng, James B. Potash, Shizhong Han. GLITTER: a web-based application for gene link inspection through tissue-specific coexpression. Scientific Reports, 2016 Sep 14;6:33460.


Contact

Please send your comments, suggestions and bug reports to Shizhong Han at: shizhong-han@uiowa.edu


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