Gene Lists

Gene lists

Purpose: Panels of genes are often important results in analysis. These gene lists can be derived by many methods (eg. differential expression, enrichment analysis, and expert knowledge). Multiple gene lists can be uploaded which will allow others to explore the genes in the list. The portal will visualize these genes within different metadata groupings provided in this file. Given groups, the actual measurement (expression) of genes in the cluster is under the control of the author and supplied in this file. Different authors may wish to use different methods to summarize genes over a group of cells (like an average, trimmed average, or median expression of the gene in cell groups), supplying those summary measurements gives you complete control over the method used.

Format: This is a tab delimited file of at least 2 columns.

Columns: The first column contains the gene names, these names should match gene names in other documents in your study. You may include an arbitrary number of genes and need not include all the genes in your study. As well, different gene lists may partially overlap as needed. The next columns are the measurement (like an average expression) of the genes in different categorical metadata groupings of interest. There can be many columns representing different categorical metadata groups.

Rows: The first row starts with the entry "GENE NAMES" and the name of the categorical groupings from metadata for which one would like to provide summary measurements (like averages within that group). Each row after the first row starts with a gene name and then the summary measurement for that gene in the cells that are a part of the metadata grouping for that column.

Example Marker Gene Lists File

Note: Not required for study visualization.

# To check the format of your file use the script verify_portal_file.py
# Requires python 3.x
python verify_portal_file.py --gene-list genes_1.txt

# Checking multiple gene lists at once
python verify_portal_file.py --gene-list genes_1.txt gene_2.txt