The “general” mode, provides search for an overview of a gene expression across different organoids compared with other types of cell culture and primary tissue.

Parameters

  • Options: Select between human and mouse samples as well as bulk and single-cell samples.

  • Gene Name / Entrez ID: Search for expression by gene name or entrez ID, searching by gene name will have an autocomplete feature after entering 2 characters.

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    “Organoid comparison” mode, shows comparison of gene expressions, pathways and cell type compositions in organoid samples to those in tissue, cell line, xenografts, etc, and compare organoids from different derivation sources or different protocols.

Parameters

  • Search By: Select to search by gene or search by organoid type.
  • Options: Select between human and mouse samples as well as bulk and single-cell samples.

  • Select Comparison Type: Query the selected comparison type.
  • Select Comparison: Query the selected comparison. Click abbrev. for list of comparison abbreviations.
  • Gene Name / Entrez ID: Search for expression by gene name or entrez ID, searching by gene name will have an autocomplete feature after entering 2 characters.
  • Select Organoid: When Search by organoid is selected, choose an organoid type.
  • Log2FC cutoff: Results will have fold-change greater than user defined threshold.
  • P-value cutoff: Results will have P-values less than user defined threshold.

  • Note: Only top 50,000 results sorted by P-value are shown.


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    “Organoid development” mode, allows finding of development-correlated genes by calculating Spearman's correlation of gene expression as organoid cultures develop over time.

Parameters

  • Search By: Select to search by gene or search by organoid type.
  • Options: Select between human and mouse samples as well as bulk and single-cell samples.

  • Gene Name / Entrez ID: Search for expression by gene name or entrez ID, searching by gene name will have an autocomplete feature after entering 2 characters.
  • Select Organoid: When Search by organoid is selected, choose an organoid type.
  • Correlation cutoff: Results will have absolute value of Spearman's correlation greater than user defined threshold.
  • P-value cutoff: Results will have P-values less than user defined threshold.

  • Note: Only top 50,000 results sorted by P-value are shown.


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    This mode will help identification of organoid specific genes in various organoid types. Organoid specificity was measured through comparison between the given organoid type and the remaining organoid types using differential expression analysis. Fold change and P-value were used to estimate the organoid specificity.

Parameters

  • Search By: Select to search by gene or search by organoid type.
  • Options: Select between human and mouse samples as well as bulk and single-cell samples.

  • Gene Name / Entrez ID: Search for expression by gene name or entrez ID, searching by gene name will have an autocomplete feature after entering 2 characters.
  • Select Organoid: When Search by organoid is selected, choose an organoid type.
  • Log2FC cutoff: Results will have fold-change greater than user defined threshold.
  • P-value cutoff: Results will have P-values less than user defined threshold.

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    This mode will help identification of tissue specific genes in various tissue types. Tissue specificity was measured through comparison between the given tissue type and the remaining tissue types using differential expression analysis. Fold change and P-value were used to estimate the tissue specificity.

Parameters

  • Search By: Select to search by gene or search by tissue type.
  • Options: Select between human and mouse samples as well as bulk and single-cell samples.

  • Gene Name / Entrez ID: Search for expression by gene name or entrez ID, searching by gene name will have an autocomplete feature after entering 2 characters.
  • Select Tissue: When Search by tissue is selected, choose a tissue type.
  • Log2FC cutoff: Results will have fold-change greater than user defined threshold.
  • P-value cutoff: Results will have P-values less than user defined threshold.

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    “Correlation analysis”, study gene-gene correlation across organoids or tissues.

Parameters

  • Search By: Select to search by similar genes or compare two genes.
  • Options: Select between human and mouse samples as well as bulk and single-cell samples.

  • Gene Name / Entrez ID: Search for expression by gene name or entrez ID, searching by gene name will have an autocomplete feature after entering 2 characters.
  • Compare with: When Compare two genes is selected, enter an additional gene name or entrez ID to see correlation with the first gene.
  • Across: See correlations across organoid or tissue types. When Organoid is selected, gene-gene correlation are calculated from the Organoid Specificity dataset. When Tissue is selected, gene-gene correlations are calculated from the Tissue Specificity dataset.
  • Select type: Correlations results are filtered by either organoid or tissue type depending on the selected Across option.
  • Correlation cutoff: Results will have absolute value of Spearman's correlation greater than user defined threshold.
  • P-value cutoff: Results will have P-values less than user defined threshold.

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Search By
Search By
Options
Organoid Specificity
organoid specificity

Gene Expression Across Tissue