General

This page provides a search function for bulkRNA-seq data.

Expression Profiling

This function is used to profile gene expression.

Basic Parameters

  • Log Scale, default=YES, type=enum, options= YES, NO
    • Whether to plot on logarithmic axis.
  • Disease Type, default=SLE, Healthy, type=list, options= SLE, Crohn, JIA, Healthy, AS, MS, UC, RA, PS, MD, PD
    • Keys for accessing dataset of disease type.
  • Gene Set, default= "STAT1, IRF1, HLA-DRB5, HLA-DPA1,HLA-F, HLA-E, HLA-C, HLA-DQB1, HLA-DQA1,HLA-DRB1, HLA-B, HLA-DRA, HLA-DPB1, HLA-A", type=text
    • Input or upload a gene set of interest, using comma or newline as delimiter.

Advanced Parameters

Dot Plot

  • Dendrogram (only pdf), default= NO, type= enum, options= YES, NO
    • If True or a valid dendrogram key, a dendrogram based on the hierarchical clustering between the groupby categories is added. Only work for pdf.
  • Standard Scale (only pdf), default=None, type=enum, options= gene, group, None
    • Whether or not to standardize the given dimension between 0 and 1, meaning for each variable or group, subtract the minimum and divide each by its maximum. Only work for pdf.
  • Cmap (only pdf), default="Reds", type=text
    • String denoting plot colormap. Only work for pdf.
  • Font Size (only pdf), default=14, type=int
  • Dot Min (only pdf), default=0.0, type=float
    • The value should be a number between 0 and 1. All fractions larger than Dot Max are clipped to this value. Only work for pdf.
  • Dot Max (only pdf), default=1.0,type=float
    • The value should be a number between 0 and 1. All fractions smaller than Dot Min are clipped to this value. Only work for pdf.

Button

  • plot    Return the interactive plot of box plot and dot plot.
  • table     Return the gene expression matrix.
  • pdf   Return the pdf of violin plot and dot plot.

Differential Genes

This function is used to find the difference genes between the two sets of data.

Basic Parameters

  • |Log2(FoldChange)| Cutoff, default=1.0, type=float
    • The screening threshold of Log2(FoldChange) of differential expression matrix.
  • p-Value Cutoff, default=0.01, type=float
    • The screening threshold of p-Value of differential expression matrix.
  • Disease Type 1, default=MS, type=list, options= SLE, Crohn, JIA, Healthy, AS, MS, UC, RA, PS, MD, PD
    • Keys for accessing dataset 1 of disease type.
  • Disease Type 2, default=Healthy, type=list, options= SLE, Crohn, JIA, Healthy, AS, MS, UC, RA, PS, MD, PD
    • Keys for accessing dataset 2 of disease type.

Advanced Parameters

Volcano Plot

  • Log2(FoldChange) Min, default=-10.0, type=float
    • Set min limit of minimum of Log2(FoldChange).
  • Log2(FoldChange) Max, default=10.0, type=float
    • Set min limit of maximum of Log2(FoldChange).
  • -Log10(p-Value) Min, default=0.0, type=float
    • Set min limit of minimum of -Log10(p-Value).
  • -Log10(p-Value) Max:, default=10.0, type=float
    • Set min limit of maximum of -Log10(p-Value).
  • Dot Size, default=5.0, type=float
    • Set the size of the points in the Volcano Plot.

Button

  • plot    Return the interactive plot of volcano plot.
  • table     Return the differential expression matrix.
  • pdf   Return the pdf of volcano plot.

Correlation Analysis

This function is used to analyze the correlation between the two groups of genes.

Basic Parameters

  • Log Scale, default=YES, type=enum, options= YES, NO
    • Whether to plot on logarithmic axis.
  • Disease Type, default=SLE, type=list, options= SLE, Crohn, JIA, Healthy, AS, MS, UC, RA, PS, MD, PD
    • Keys for accessing dataset of disease type.
  • Correlation Method, default=Pearson, type=enum, options= Pearson, Spearman, Kendall
  • Gene Set 1, default= "STAT1, IRF1, HLA-DRB5, HLA-DPA1,HLA-F, HLA-E, HLA-C, HLA-DQB1, HLA-DQA1,HLA-DRB1, HLA-B, HLA-DRA, HLA-DPB1, HLA-A", type= text
    • Input or upload a gene set 1 of interest, using comma or newline as delimiter.
  • Gene Set 2, default= "HLA-DQB1-AS1,HLA-DQA2, PSMC4, RNF5, HSPA1B, CNDP2, PSMB9, CTNNBL1,PSME1", type=text
    • Input or upload a gene set 2 of interest, using comma or newline as delimiter.

Advanced Parameters

Regression Plot

  • Dot Size, default= 5, type= int
    • Set the size of the points in the Regression Plot.
  • Line Size, default= 2, type= int
    • Set the thickness of the line in the Regression Plot.
  • Dot Color, default= #4169E1, type= hex code
    • Set the color of the dot in the Regression Plot.
  • Line Color, default= #DC143C, type= hex code
    • Set the color of the line in the Regression Plot.
  • Label (only pdf), default=YES, type=enum, options= YES, NO
    • Whether to show the label in the Regression Plot. Only work for pdf.
Heatmap
  • Legend Min, default= -1.0, type= float
    • Set min limit of minimum of correlation coefficient.
  • Legend Max, default= 1.0, type= float
    • Set min limit of maximum of correlation coefficient.
  • Cmap (only pdf), default="Reds", type=text
    • String denoting plot colormap. Only work for pdf.

Button

  • plot    Return the interactive plot of regression plot and heatmap.
  • table     Return the average expression matrix of two gene sets.
  • pdf   Return the pdf of regression plot and heatmap.

Similar Gene Detection

This function is used to find a similar expression pattern with a gene in different disease types.

Basic Parameters

  • Top Number, default= 100, type= int
    • Specify the number of genes with the highest correlation coefficient.
  • Correlation Method, default=Pearson, type=enum, options= Pearson, Spearman, Kendall
  • Disease Type, default=SLE, type=list, options= SLE, Crohn, JIA, Healthy, AS, MS, UC, RA, PS, MD, PD
    • Keys for accessing dataset of disease type.
  • Log Scale, default=YES, type=enum, options= YES, NO
    • Whether to plot on logarithmic axis.
  • Gene Set, default= "STAT1, IRF1, HLA-DRB5, HLA-DPA1, HLA-F, HLA-E, HLA-C, HLA-DQB1, HLA-DQA1, HLA-DRB1, HLA-B, HLA-DRA, HLA-DPB1, HLA-A", type=text
    • Input or upload a gene set of interest, using comma or newline as delimiter.

Button

  • table     Return a list of similar gene.

General

This page provides a search function for scRNA-seq data. Besides, it can also perform grouping statistics on cells and display dimensionality reduction by UMAP.

Basic Parameters

  • Downsample, default= 10%, type= enum, options= 5%, 10%, 20%, 50%, 100%
    • Proportion of cells stratified sampling based on data set and cell type.
  • Groupby, default= Celltype, type= enum, options= Disease, Tissue, Celltype, Dataset
    • The key of the observation grouping to consider.
  • Disease-Tissue Type , default= MS-PBMC, type= list, options= Healthy-Colon, Healthy-Ileum, Healthy-LaminaPropria, Healthy-Lung, Healthy-PBMC, Healthy-Rectum, MS-PBMC, SLE-PBMC, SSc-Lung, SjS-PBMC, UC-Colon, UC-LaminaPropria, UC-PBMC, UC-Rectum
    • Keys for accessing dataset of disease and tissue type.
  • Cell Type, default= B_cell, CD14_Mono, CD16_Mono, CD4_T, CD8_T, type= list, options= B_cell, CD14_Mono, CD16_Mono, CD4_T, CD8_T, Endothelial_cells, Epithelial_cells, Macrophage, NK_cell, Smooth_muscle_cells
    • Keys for accessing dataset of cell type.

Advanced Parameters

  • Dot Size, default=2.0, type=float
    • Set the size of the points in the UMAP Plot.

Button

  • plot    Return the interactive plot of UMAP plot and bar plot.
  • pdf   Return the pdf of UMAP plot and bar plot.

Expression Profiling

This function is used to profile gene expression.

Basic Parameters

  • Downsample, default= 100%, type= enum, options= 5%, 10%, 20%, 50%, 100%
    • Proportion of cells stratified sampling based on data set and cell type.
  • Log Scale, default=YES, type=enum, options= YES, NO
    • Whether to plot on logarithmic axis.
  • Groupby, default= Disease, type= enum, options= Disease, Tissue, Celltype
    • The key of the observation grouping to consider.
  • Plot Umap, default= NO, type= enum, options= YES, NO
    • Decide whether to draw umap plot.
  • Disease-Tissue Type , default= Healthy-PBMC, MS-PBMC, type= list, options= Healthy-Colon, Healthy-Ileum, Healthy-LaminaPropria, Healthy-Lung, Healthy-PBMC, Healthy-Rectum, MS-PBMC, SLE-PBMC, SSc-Lung, SjS-PBMC, UC-Colon, UC-LaminaPropria, UC-PBMC, UC-Rectum
    • Keys for accessing dataset of disease and tissue type.
  • Cell Type, default= Macrophage, type= list, options= B_cell, CD14_Mono, CD16_Mono, CD4_T, CD8_T, Endothelial_cells, Epithelial_cells, Macrophage, NK_cell, Smooth_muscle_cells
    • Keys for accessing dataset of cell type.
  • Gene Set, default= "STAT1, IRF1, HLA-DRB5, HLA-DPA1, HLA-F, HLA-E, HLA-C, HLA-DQB1, HLA-DQA1, HLA-DRB1, HLA-B, HLA-DRA, HLA-DPB1, HLA-A", type=text
    • Input or upload a gene set of interest, using comma or newline as delimiter.

Advanced Parameters

Dot Plot

  • Dendrogram (only pdf), default= NO, type= enum, options= YES, NO
    • If True or a valid dendrogram key, a dendrogram based on the hierarchical clustering between the groupby categories is added. Only work for pdf.
  • Standard Scale (only pdf), default=None, type=enum, options= gene, group, None
    • Whether or not to standardize the given dimension between 0 and 1, meaning for each variable or group, subtract the minimum and divide each by its maximum. Only work for pdf.
  • Cmap (only pdf), default=Reds, type=text
    • String denoting plot colormap. Only work for pdf.
  • Font Size (only pdf), default=14, type=int
  • Dot Min (only pdf), default=0.0, type=float
    • The value should be a number between 0 and 1. All fractions larger than Dot Max are clipped to this value. Only work for pdf.
  • Dot Max (only pdf), default=1.0,type=float
    • The value should be a number between 0 and 1. All fractions smaller than Dot Min are clipped to this value. Only work for pdf.
UMAP Plot
  • Dot Size, default=2.0, type=float
    • Set the size of the points in the UMAP Plot.
  • Cmap (only pdf), default="Reds", type=text
    • String denoting plot colormap. Only work for pdf.

Button

  • plot    Return the interactive plot of box plot, dot plot and UMAP plot.
  • table     Return the gene expression matrix.
  • pdf   Return the pdf of box plot, dot plot and UMAP plot.

Differential Genes

This function is used to find the difference genes between the two sets of data.

Basic Parameters

  • Downsample, default= 100%, type= enum, options= 5%, 10%, 20%, 50%, 100%
    • Proportion of cells stratified sampling based on data set and cell type.
  • |Log2(FoldChange)| Cutoff, default=1.0, type=float
    • The screening threshold of Log2(FoldChange) of differential expression matrix.
  • p-Value Cutoff, default=0.01, type=float
    • The screening threshold of p-Value of differential expression matrix.
  • Disease-Tissue Type 1, default= MS-PBMC, type= list, options= Healthy-Colon, Healthy-Ileum, Healthy-LaminaPropria, Healthy-Lung, Healthy-PBMC, Healthy-Rectum, MS-PBMC, SLE-PBMC, SSc-Lung, SjS-PBMC, UC-Colon, UC-LaminaPropria, UC-PBMC, UC-Rectum
    • Keys for accessing dataset 1 of disease and tissue type.
  • Disease-Tissue Type 2, default= MS-PBMC type= list, options= Healthy-Colon, Healthy-Ileum, Healthy-LaminaPropria, Healthy-Lung, Healthy-PBMC, Healthy-Rectum, MS-PBMC, SLE-PBMC, SSc-Lung, SjS-PBMC, UC-Colon, UC-LaminaPropria, UC-PBMC, UC-Rectum
    • Keys for accessing dataset 2 of disease and tissue type.
  • Cell Type 1, default= B_cell, type= list, options= B_cell, CD14_Mono, CD16_Mono, CD4_T, CD8_T, Endothelial_cells, Epithelial_cells, Macrophage, NK_cell, Smooth_muscle_cells
    • Keys for accessing dataset 1 of cell type.
  • Cell Type 2, default= Macrophage, type= list, options= B_cell, CD14_Mono, CD16_Mono, CD4_T, CD8_T, Endothelial_cells, Epithelial_cells, Macrophage, NK_cell, Smooth_muscle_cells
    • Keys for accessing dataset 2 of cell type.

Advanced Parameters

Volcano Plot

  • Log2(FoldChange) Min, default=-10.0, type=float
    • Set min limit of minimum of Log2(FoldChange).
  • Log2(FoldChange) Max, default=10.0, type=float
    • Set min limit of maximum of Log2(FoldChange).
  • -Log10(p-Value) Min, default=0.0, type=float
    • Set min limit of minimum of -Log10(p-Value).
  • -Log10(p-Value) Max:, default=20.0, type=float
    • Set min limit of maximum of -Log10(p-Value).
  • Dot Size, default=5.0, type=float
    • Set the size of the points in the Volcano Plot.

Button

  • plot    Return the interactive plot of volcano plot.
  • table     Return the differential expression matrix.
  • pdf   Return the pdf of volcano plot.

Correlation Analysis

This function is used to analyze the correlation between the two groups of genes.

Basic Parameters

  • Downsample, default= 10%, type= enum, options= 5%, 10%, 20%, 50%, 100%
    • Proportion of cells stratified sampling based on data set and cell type.
  • Log Scale, default=YES, type=enum, options= YES, NO
    • Whether to plot on logarithmic axis.
  • Disease-Tissue Type , default= SLE-PBMC, type= list, options= Healthy-Colon, Healthy-Ileum, Healthy-LaminaPropria, Healthy-Lung, Healthy-PBMC, Healthy-Rectum, MS-PBMC, SLE-PBMC, SSc-Lung, SjS-PBMC, UC-Colon, UC-LaminaPropria, UC-PBMC, UC-Rectum
    • Keys for accessing dataset of disease and tissue type.
  • Cell Type, default= CD14_Mono, CD16_Mono, type= list, options= B_cell, CD14_Mono, CD16_Mono, CD4_T, CD8_T, Endothelial_cells, Epithelial_cells, Macrophage, NK_cell, Smooth_muscle_cells
    • Keys for accessing dataset of cell type.
  • Correlation Method, default=Pearson, type=enum, options= Pearson, Spearman, Kendall
  • Gene Set 1, default= "STAT1, IRF1, HLA-DRB5, HLA-DPA1, HLA-F, HLA-E, HLA-C, HLA-DQB1, HLA-DQA1, HLA-DRB1, HLA-B, HLA-DRA, HLA-DPB1, HLA-A", type= text
    • Input or upload a gene set 1 of interest, using comma or newline as delimiter.
  • Gene Set 2, default= "HLA-DQB1-AS1, HLA-DQA2, PSMC4, RNF5, HSPA1B, CNDP2, PSMB9, CTNNBL1, PSME1", type=text
    • Input or upload a gene set 2 of interest, using comma or newline as delimiter.

Advanced Parameters

Regression Plot

  • Dot Size, default= 5.0, type= float
    • Set the size of the points in the Regression Plot.
  • Line Size, default= 2, type= int
    • Set the thickness of the line in the Regression Plot.
  • Dot Color, default= #4169E1, type= hex code
    • Set the color of the dot in the Regression Plot.
  • Line Color, default= #DC143C, type= hex code
    • Set the color of the line in the Regression Plot.
  • Label (only pdf), default=YES, type=enum, options= YES, NO
    • Whether to show the label in the Regression Plot. Only work for pdf.
Heatmap
  • Legend Min, default= -1.0, type= float
    • Set min limit of minimum of correlation coefficient.
  • Legend Max, default= 1.0, type= float
    • Set min limit of maximum of correlation coefficient.
  • Cmap (only pdf), default="RdBu_r", type=text
    • String denoting plot colormap. Only work for pdf.

Button

  • plot    Return the interactive plot of regression plot and heatmap.
  • table     Return the average expression matrix of two gene sets.
  • pdf   Return the pdf of regression plot and heatmap.

Cell-cell Interaction

This function is used to show the communication between different cell types.

Basic Parameters

  • Disease-Tissue Type , default= SLE-PBMC, type= enum, options= Healthy-Colon, Healthy-Ileum, Healthy-LaminaPropria, Healthy-Lung, Healthy-PBMC, Healthy-Rectum, MS-PBMC, SLE-PBMC, SSc-Lung, SjS-PBMC, UC-Colon, UC-LaminaPropria, UC-PBMC, UC-Rectum
    • Keys for accessing dataset of disease and tissue type.
  • Cell Type, default= B_cell, CD14_Mono, CD16_Mono, Macrophage, type= list, options= B_cell, CD14_Mono, CD16_Mono, CD4_T, CD8_T, Endothelial_cells, Epithelial_cells, Macrophage, NK_cell, Smooth_muscle_cells
    • Keys for accessing dataset of cell type.
  • p-Value Cutoff, default=0.05, type=float
    • The screening threshold of p-Value of cell-cell communication matrix.
  • Mean Cutoff, default=0.8, type=float
    • The screening threshold of Mean Expression of cell-cell communication matrix.

Advanced Parameters

Circos Plot

  • Mean Cutoff (display name), default=0.9, type=float
    • The threshold of Mean Expression of cell-cell communication matrix to decide whether to display gene name.

Button

  • plot    Return the interactive plot of circos plot and heatmap.
  • table     Return the cell-cell communication matrix.