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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About PCTanno

The atlas of critical transition in cancer: from pre-cancerous lesions (pink) to local malignancy(green), invading through the basement membrane into deeper tissue layers. This transition involves complex interactions between pre-malignant, malignant, and/or non-malignant cells within the tumor ecosystem.

The PCTanno database includes 62 datasets from 57 single cell RNA-sequencing (RNA-seq) studies, 12 whole exome sequencing (WES), 12 bulk RNA-seq datasets that across 13 organs from healthy to premalignant lesion to cancer. We carried out functional impact prediction of mutations. PCTanno provides systematic functional annotations of the dynamic biological processes involved in tumorigenesis, including the cell annotations, cell composition by disease state, uniform manifold approximation and projection (UMAP) plots, inferred CNV and somatic mutations, differentiation trajectory inference, cell-cell communication, gene regulatory network inference, gene ontology and pathway enrichment analysis. The application of PCTanno will help to identify novel biomarkers across transitions from healthy to diseased tissues, and dissect the sequential molecular and cellular events that promote oncogenesis leading to precision prevention and interception strategies.

∗Logo description: The atlas of critical transition in cancer: from pre-cancerous lesions (pink) to local malignancy(green), invading through the basement membrane into deeper tissue layers. This transition involves complex interactions between pre-malignant, malignant, and/or non-malignant cells within the tumor ecosystem.

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Examples: Gene symbol: HNF4A, Entrez gene ID: 3172

                        Gene-related functional analyses include:
                                                • Malignant transformation analysis.
                                                • Malignant transformation related pathway analysis.
                                                • Cell-cell communication analysis.
                                                • Single-cell gene regulatory network inference analysis.
                                                • Somatic mutation of malignant transformation related genes.
                                                • Related drugs of malignant transformation related genes.
bullet pointSearch by tissue

                        Tissue-related functional analyses include:
                                                • Annotation details for different cell compartments.
                                                • Cell type statistics by disease state.
                                                • Cell type dynamics in malignant transformation.
                                                • Cell lineage trajectory inference.
                                                • TF regulatory network analysis.
                                                • Cell-cell interactions analysis.
                                                • Stemness, Senescence, Metaplasia and NeoTCR signature analysis.
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We performed expression dynamics analysis to delineate transcriptomic changes that occur on the phenotypic continuum from healthy tissues to invasive carcinoma. And we detected 14,193 unique genes in 13 human tissues. For each tissue type, the malignant transformation related genes are listed as below (Tissue: number of malignant transformation related genes).


Breast icon - An image representing breast tissue. This image is associated with Breast, indicating the number of occurrences or references related to breast in the context.

Breast (H: 1595)

 Cervix icon - An image representing Cervix tissue. This image is associated with Cervix, indicating the number of occurrences or references related to Cervix in the context.

Cervix (H: 2539)

 Colorectum icon - An image representing Colorectum tissue. This image is associated with Colorectum, indicating the number of occurrences or references related to Colorectum in the context.

Colorectum (H: 4577)

 Endometrium icon - An image representing Endometrium tissue. This image is associated with Endometrium, indicating the number of occurrences or references related to Endometrium in the context.

Endometrium (H: 2407)
Esophagus icon - An image representing Esophagus tissue. This image is associated with Esophagus, indicating the number of occurrences or references related to Esophagus in the context.

Esophagus (H: 9823)

 Liver icon - An image representing Liver tissue. This image is associated with Liver, indicating the number of occurrences or references related to Liver in the context.

Liver (H: 9332)

 Lung icon - An image representing Lung tissue. This image is associated with Lung, indicating the number of occurrences or references related to Lung in the context.

Lung (H: 2380)

 Oral cavity icon - An image representing Oral cavity tissue. This image is associated with Oral cavity, indicating the number of occurrences or references related to Oral cavity in the context.

Oral cavity (H: 8304)

 Pancreas icon - An image representing Pancreas tissue. This image is associated with Pancreas, indicating the number of occurrences or references related to Pancreas in the context.

Pancreas(H: 1962)
Skin icon - An image representing Skin tissue. This image is associated with Skin, indicating the number of occurrences or references related to Skin in the context.

Skin (H: 5524)

 Stomach icon - An image representing Stomach tissue. This image is associated with Stomach, indicating the number of occurrences or references related to Stomach in the context.

Stomach (H: 1310)

 Thyroid icon - An image representing Thyroid tissue. This image is associated with Thyroid, indicating the number of occurrences or references related to Thyroid in the context.

Thyroid (H: 7159)

 Prostate icon - An image representing Prostate tissue. This image is associated with Prostate, indicating the number of occurrences or references related to Prostate in the context.

Prostate (H: 2977)