Extensive Ramp Sequence Data
Extensive Ramp Sequence Data
These data explain how ramp sequences correlate with gene expression (not detected, low, medium, high) within tissues and cell types.
Ramp Count per Cell/Tissue by Gene Expression
The number of ramps in every tissue/cell type spread by gene expression (not detected, low, medium, high) including a chi-squared analysis for each tissue/cell type to test if ramps correlate with expression. These comma-separated files include the tissue/cell type, counts of ramps by expression, counts of genes with no ramp by expression, total genes, percent of ramps, expected ramp counts by expression, expected ramps subtracted from the observed counts, and a chi-squared p-value for each tissue/cell type.
Ramp Count per Gene by Gene Expression
The number of ramps in every gene—based on either tissue or cell stratified RSCU values—spread by gene expression (not detected, low, medium, high). These comma-separated files include the gene name, counts of ramps by expression, counts of genes with no ramp by expression, total ramps, and total genes
Probability of Ramp Given Gene Expression
The probability of a ramp given a gene expression (not detected, low, medium, high) for every gene based on either tissue or cell stratified RSCU values, calculated using Bayes theorem. These comma-separated files include the gene name, probability of a ramp given each of the four levels of gene expression, and a column to determine if the ramps correlate with higher expression (P(ramp|high expression) – weighted average (P(ramp|non detected expression) and P(ramp|low expression)) given that the weighted average < P(ramp|medium expression) < high. Any gene not following this pattern was given a value of -1).
These files contain pairwise z-test analyses between every tissue/cell type to test for different use of ramp sequences, as well as which tissues/cells use of ramp sequences are most different from others.
Pairwise Z-Test
Pairwise z-tests between every tissue/cell type to test for different percentages of ramp sequences. These comma-separated files include the names of the two tissues/cells being compared, a z-test statistic, and a p-value per comparison.
Percent Significant Z-Tests
Which tissues/cells use of ramp sequences are most different from others, computed using the percent of significant pairwise z-tests confirming different ramp percentages. This comma-separated file includes the name of a tissue/cell type, the total number of ramps in that tissue/cell type, the total number of genes, the number of pairwise tests in which it significantly differed from another tissue, and that count of significant tests as a percent of total comparisons.
The total number of genes and genes with ramps for each tissue/cell type, including a chi squared analysis to determine if across all tissues/cells there is a difference in ramp percentage.
Ramps in Genes by Tissue/Cell Type
All genes and whether of not they have a ramp for any given tissue/cell type. This comma-separated file includes an Ensembl gene identifier, the name of a gene, a tissue type, a cell type, an expression level, a reliability score, and whether a ramp is present.
Total Genes and Ramps
The total number of genes and ramps for each tissue/cell type, including a chi squared analysis to determine if across all tissues/cells there is a difference in ramp percentage. This comma-separated file includes a tissue/cell type, the total number of genes, the total ramps, the expected number of ramps based on an even distribution of ramps across all tissues/cells, and observed minus expected number of ramps, and a chi-squared test statistic. Along the bottom are several column totals, the average percent of ramps across all tissues/cells, and the chi-squared p-value.
Percentage of Ramps Shared Between Tissues
Comparisons between every tissue in a dataset of which genes have ramp sequences. Each tissue comparison includes data on the percentage of ramp sequences that are present in both tissues, the number of ramp sequences in that are present in both tissues, the total number of genes with a ramp sequence in at least one of the tissues, and
These files indicate the expression level and if a ramp sequence is present for each gene, specific to the indicated tissue type.
Select a tissue to download:
Several files that contain information on ramp sequence presence across 62 human tissues (from the consensus dataset) in both SARS-CoV-2 genome and human genes encoding SARS-CoV-2 entry factors.
Ramp sequence presence in seven SARS-CoV-2 genes across 62 tissues (consensus dataset).
Ramp sequence presence in seven Human entry factors for SARS-Cov-2, across 62 tissues (consensus dataset).
The percentages of ramp sequences that are shared between any two tissues (all datasets).