GeneBot Functions

Gene Summary

GeneBot enables users to submit a human gene of interest and outputs information pertaining to the searched gene. The /gene command provides a summary about the gene and links to various databases.

The summary outputted is retrieved using the NCBI Entrez Gene database API. Links are provided to gene landing pages from various genomic tools that the Ma’ayan Lab developed, including Harmonizome, ARCHS4, and Geneshot.

✦ Input Format: /gene <gene name>

✦ Example:

  • Input: /gene TP53
  • Output: image

Gene Enrichment Analysis

GeneBot enables users to submit a gene set for enrichment analysis. The /geneset command can be used to perform gene enrichment analysis by listing valid Entrez human gene symbols following the command. Alternatively, users can upload a CSV file with the gene set for analysis by calling @genebot. Additionally, users can specify which gene-set library they want to be displayed in their results in Slack.

The gene set is analyzed using the Enrichr API. The bot will output a link to Enrichr for the gene set entered as well as summary statistics about the gene set. A bar graph displaying the top 10 enriched terms for the user selected gene-set library will be attached as a pdf file.

✦ Input Format:

  • Input (no library specified):
    • /geneset gene1, gene2, gene3...
  • Input (library specified):
    • /geneset [library, gene1, gene2, gene3...]
      • Gene list can be space or comma separated.
      • Library specified input must be contained by brackets.
  • Input (file upload):
    • @genebot set *file*
    • @genebot set library *file*
      • Here is a sample file that is properly formatted with a gene set.

✦ Example:

  • Input: /geneset MAPK3, STAT1, CREB1
  • Output: image

✦ Gene Libraries: When specifying a library for output, GeneBot will recognize full Enrichr library names or predefined short hands. Full Enrichr library names can be found here. Library short hands are available for several widely-used gene set libraries.

  • Library short hands include:
    • GO = GO_Biological_Process_2018
    • MGI = MGI_Mammalian_Phenotype_Level_4_2019
    • KEGG = KEGG_2019_Human
    • CHEA = ChEA_2016
    • ENCODE = ENCODE_TF_ChIP-seq_2015
    • GWAS = GWAS_Catalog_2019

Gene-Gene Network Analysis

GeneBot enables users to submit a gene set for gene-gene network analysis based on protein-protein interactions (PPI) and gene-gene co-expression. When users enter a gene set, the /network command can be used to trigger the constructions of a gene-gene network.

The gene set is analyzed using the Genes2Networks API to generate a PPI subnetwork that connects the genes and proteins with known protein-protein interactions and gene-gene co-expression associations. Co-expression correlations are determined via a human gene correlation matrix from ARCHS4 to find the top 5 most correlated genes to each input gene. The bot will output summary statistics about the gene set. A network graph displaying the interactions between the input genes will be attached as a PDF file.

✦ Input Format:

  • Input: /network gene1, gene2, gene3...

✦ Example:

  • Input: /network BRCA1, BRCA2, STAT1, MAPK3
  • Output: image

Gene Learning Game

GeneBot also contains an interactive game that can be played to learn how to memorize gene names and their known functions. We created the /learn command to output a multiple choice question where users can match the correct summary to the gene in question.

✦ Example:

  • Input: /learn-genes
  • Output: image

Help Commands:

A list of all commands can by accessed by calling: @genebot help

✦ Gene Summary Help: If a user needs help with using the /gene command to retrieve a summary about a gene, they can call the following command /gene-help.

✦ Enrichment Analysis Help: There are several built in help commands for performng enrichment analysis with GeneBot that can be called in Slack to provide concise summaries about different app features and functions. A list of all enrichment analysis help commands can be found by calling: /geneset-help

  • /geneset-help ? → provides summary of how to use GeneBot for enrichment analysis
  • /geneset-help library? → provides instructions on how to specify library for output
  • /geneset-help fileupload? → provides instructions on how to upload file for analysis
  • /geneset-help slashcommand? → provides instructions on how to navigate /geneset command

✦ Gene-Gene Network Help: If a user needs help with using the /network command to retrieve a summary about a gene, they can call the following command /network-help.

If you have any questions about how to use GeneBot, please contact us at maayanlabapps@gmail.com.