Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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Instructions for Navigating the Site

1. PCTanno information
2. Understanding gene annotation of PCTanno
    a. Search by Gene symbol or Entrez gene ID, example: Gene symbol: HNF4A, Entrez gene ID: 3172
    b. Gene search result page
    c. Gene annotation result page
        i. Gene summary
        ii. Malignant transformation analysis
        iii. Malignant transformation related pathway analysis
        iv. Cell-cell communication analysis
        v. Single-cell gene regulatory network inference analysis
        vi. Somatic mutation of malignant transformation related genes
        vii. Related drugs of malignant transformation related genes
3. Understanding tissue annotation of PCTanno
    a. Search by tissue, example: Liver
    b. Tissue annotation result page
        i. Tissue samples summary
        ii. Annotation details for different cell compartments
        iii. Cell type statistics by disease state
        iv. Cell type dynamics in malignant transformation
        v. Cell lineage trajectory inference
        vi. TF regulatory network analysis
        vii. Cell-cell interaction analysis
        viii. Stemness, Senescence, Metaplasia and NeoTCR signature analysis
4. Download data and contact us

bullet point 1. PCTanno information
We analyzed 2 datasets from 52 single cell RNA sequencing (scRNA-seq) studies and 12 whole exome sequencing (WES) datasets that across 12 tissues from healthy to premalignant lesion to cancer.

bullet point 2. Understanding gene annotation of PCTanno
bullet point a. Search by Gene symbol or Entrez gene ID, example: Gene symbol: HNF4A, Entrez gene ID: 3172
 - Input query: Gene symbol or Entrez gene ID.
Search page of HNF4A - An image showing the gene search bar of searching example gene HNF4A. The user can search the gene via Gene symbol: HNF4A or Entrez gene ID: 3172
bullet point b. Gene search result page
 This image shows the gene list according to your search.
Search result of HNF4A - An image showing the search result of HNF4A, including Gene ID, Gene Symbol, Chromosome, Species, Tissue, PMID and Adj P-value

bullet point c. Gene annotation result page
 This image shows PCTanno's annotation categories for your query with links to their corresponding annotation parts.
Annotation of PCTanno includes Gene summary, Malignant transformation analysis, Malignant transformation related pathway analysis, Cell-cell communication analysis, Single-cell gene regulatory network inference analysis and Related drugs of malignant transformation related genes.

bullet point i. 'Gene summary' category
This image category shows the information of the PCTanno.
Summary of HNF4A - An image showing the overall information of HNF4A such as Species, Gene symbol, Gene ID, Gene name, Gene Alias, Cytomap, Gene Type, GO ID and UniProtAcc
bullet point ii. 'Malignant transformation analysis' category
This image category provides the result of Malignant transformation analysis.
Malignant transformation involving gene list - An image showing the basic information of the gene involved in the malignant transformation, including Entrez ID, Symbol, Replicates, Species, Organ, Tissue, Adj P-value, Log2FC and Malignancy Transcriptomic changes along malignancy continuum - An image showing the dynamic expression of HNF4A in different tissues and it give the detailed disease stages in each tissue
bullet point iii. 'Malignant transformation related pathway analysis' category
This image category provides the result of malignant transformation related pathway analysis.
Biological process and pathway - An image showing the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer
Biological process and pathway - An image showing the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer
Biological process and pathway - An image showing the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer
bullet point iv. 'Cell-cell communication analysis' category
This image category provides the result of cell-cell communication analysis.
                   Note: There is no result of HNF4A in this category. Here is the result of ITGB1 as an example.
Gene function of HNF4A - An image showing the gene function analysis result of HNF4A as ligand/receptor in single cell transcriptome. The result includes Entrez ID, Symbol, Replicates, Species, Organ, Tissue, Adj P-value, Log2FC and Malignancy
bullet point v. 'Single-cell gene regulatory network inference analysis' category
This image category provides the result of single-cell gene regulatory network inference analysis.
Transcription factor - An image showing the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states
bullet point vi. 'Somatic mutation of malignant transformation related genes' category
This image category provides the somatic mutation of malignant transformation related genes.
Related drugs - An image showing the chemicals and drugs interact with genes involved in malignant transfromation, the information of the related drugs includes Entrez ID, Symbol, Category, Interaction Types, Drug Claim Name, Drug Name and PMIDs
bullet point vii. 'Related drugs of malignant transformation related genes' category
This image category provides the related drugs of malignant transformation related genes.
Related drugs - An image showing the chemicals and drugs interact with genes involved in malignant transfromation, the information of the related drugs includes Entrez ID, Symbol, Category, Interaction Types, Drug Claim Name, Drug Name and PMIDs

bullet point 3. Understanding tissue annotation of PCTanno
bullet point a. Search by tissue, example: Liver
 Select your interested tissue.
Search page of Stomach- An image showing the tissue search bar of searching example tissue: Liver

bullet point b. Tissue annotation result page
 This image shows the tissue annotation of PCTanno for your query with links to their corresponding annotation parts.
Tissue Annotation of PCTanno includes Tissue samples summary, Annotation details for different cell compartments, Cell type statistics by disease stage, Cell type dynamics in malignant transformation, Cell lineage trajectory inference, Gene regulatory network analysis, Cell-cell interaction analysis and Stemness, Senescence, metaplasia signature analysis
bullet point i. 'Tissue samples summary' category
This image category provides the tissue samples summary.
Tissue samples summary - An image showing the overall information of tissue Stomach such as Tissue name, Disease Stage, Replicates, Epithelia UMAP, PMID, Source and Platform Tissue samples summary - An image showing the overall information of tissue Stomach such as Tissue name, Disease Stage, Replicates, Epithelia UMAP, PMID, Source and Platform
bullet point ii. 'Annotation details for different cell compartments' category
This image category provides the annotation details for different cell compartments.
Annotation details for different cell compartments - An image showing the cell compartment of different cell types, including epithelial cells, Immune cells and Stromal cells Annotation details for different cell compartments - An image showing the cell compartment of different cell types, including epithelial cells, Immune cells and Stromal cells

bullet point iii. 'Cell type statistics by disease state' category
This image category provides the cell type statistics by disease state.
Cell type statistics by disease stage - An image showing cell fraction of different disease stages in different cell types, including epithelial cells, Immune cells and Stromal cells
bullet point iv. 'Cell type dynamics in malignant transformation' category
This image category provides the cell type dynamics in malignant transformation.
Cell type dynamics in malignant transformation - An image showing the fraction of cell type in each scRNA-seq sample plotted against position of the sample in the malignancy continuum for all cell types in Stomach tissue
bullet point v. 'Cell lineage trajectory inference' category
This image category provides the result cell lineage trajectory inference.
Cell lineage trajectory inference - An image showing the inferred cell linaege trajectory of cells from the datasets of Stomach tissue
bullet point vi. 'TF regulatory network analysis' category
This image category provides the result of TF regulatory network analysis.
Gene regulatory network analysis - An image showing heatmap representation of significantly different TFs among all cell types of epithelial, Immune and Stromal compartment in different disease stage-derived samples of Stomach tissue by comparing their average AUC by using pySCENIC in Python
bullet point vii. 'Cell-cell interaction analysis' category
This image category provides the result of cell-cell interaction analysis.
Cell-cell interaction analysis - An image showing the cell-cell communications between each two interacting cell types in different disease stage-derived samples of Stomach tissue. For a given cell type, different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.
Cell-cell interaction analysis - An image showing the cell-cell communications between each two interacting cell types in different disease stage-derived samples of Stomach tissue. For a given cell type, different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.
Cell-cell interaction analysis - An image showing the cell-cell communications between each two interacting cell types in different disease stage-derived samples of Stomach tissue. For a given cell type, different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.
bullet point viii. 'Stemness, Senescence, Metaplasia and NeoTCR signature analysis' category
This image category provides the result of Stemness, Senescence, Metaplasia and NeoTCR signature analysis.
Stemness, Senescence, metaplasia signature analysis - An image showing the analysis results of stemness, senescence, and metaplasia signatures
Stemness, Senescence, metaplasia signature analysis - An image showing the analysis results of stemness, senescence, and metaplasia signatures
Stemness, Senescence, metaplasia signature analysis - An image showing the analysis results of stemness, senescence, and metaplasia signatures
bullet point 3. Download data and contact us
Please go to download page and contact page.