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Gene: CST3 |
Gene summary for CST3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CST3 | Gene ID | 1471 |
| Gene name | cystatin C | |
| Gene Alias | ARMD11 | |
| Cytomap | 20p11.21 | |
| Gene Type | protein-coding | GO ID | GO:0001974 | UniProtAcc | A0A0K0K1J1 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 1471 | CST3 | GSM4909277 | Human | Breast | Precancer | 3.80e-04 | -8.89e-01 | 0.0177 |
| 1471 | CST3 | GSM4909282 | Human | Breast | IDC | 1.04e-27 | 6.27e-01 | -0.0288 |
| 1471 | CST3 | GSM4909285 | Human | Breast | IDC | 7.49e-07 | -3.37e-01 | 0.21 |
| 1471 | CST3 | GSM4909286 | Human | Breast | IDC | 3.50e-25 | 6.68e-01 | 0.1081 |
| 1471 | CST3 | GSM4909291 | Human | Breast | IDC | 1.73e-02 | 3.32e-01 | 0.1753 |
| 1471 | CST3 | GSM4909293 | Human | Breast | IDC | 9.19e-08 | 2.32e-01 | 0.1581 |
| 1471 | CST3 | GSM4909294 | Human | Breast | IDC | 1.06e-08 | -4.61e-01 | 0.2022 |
| 1471 | CST3 | GSM4909296 | Human | Breast | IDC | 1.51e-23 | -6.48e-01 | 0.1524 |
| 1471 | CST3 | GSM4909297 | Human | Breast | IDC | 2.79e-24 | 4.06e-01 | 0.1517 |
| 1471 | CST3 | GSM4909298 | Human | Breast | IDC | 1.48e-50 | 8.79e-01 | 0.1551 |
| 1471 | CST3 | GSM4909301 | Human | Breast | IDC | 3.63e-26 | 5.96e-01 | 0.1577 |
| 1471 | CST3 | GSM4909302 | Human | Breast | IDC | 5.19e-05 | 3.43e-01 | 0.1545 |
| 1471 | CST3 | GSM4909306 | Human | Breast | IDC | 1.89e-10 | 4.73e-01 | 0.1564 |
| 1471 | CST3 | GSM4909307 | Human | Breast | IDC | 3.66e-29 | 6.55e-01 | 0.1569 |
| 1471 | CST3 | GSM4909308 | Human | Breast | IDC | 4.86e-113 | 1.10e+00 | 0.158 |
| 1471 | CST3 | GSM4909311 | Human | Breast | IDC | 1.80e-32 | -6.04e-02 | 0.1534 |
| 1471 | CST3 | GSM4909312 | Human | Breast | IDC | 3.86e-19 | 4.43e-01 | 0.1552 |
| 1471 | CST3 | GSM4909315 | Human | Breast | IDC | 4.37e-17 | -5.87e-01 | 0.21 |
| 1471 | CST3 | GSM4909316 | Human | Breast | IDC | 6.38e-06 | -6.75e-01 | 0.21 |
| 1471 | CST3 | GSM4909319 | Human | Breast | IDC | 1.95e-53 | 3.46e-01 | 0.1563 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00430624 | Esophagus | ESCC | extracellular structure organization | 171/8552 | 302/18723 | 7.73e-05 | 5.76e-04 | 171 |
| GO:00452294 | Esophagus | ESCC | external encapsulating structure organization | 172/8552 | 304/18723 | 7.80e-05 | 5.80e-04 | 172 |
| GO:0045861111 | Esophagus | ESCC | negative regulation of proteolysis | 195/8552 | 351/18723 | 1.13e-04 | 7.85e-04 | 195 |
| GO:0051346110 | Esophagus | ESCC | negative regulation of hydrolase activity | 208/8552 | 379/18723 | 1.76e-04 | 1.14e-03 | 208 |
| GO:19011362 | Esophagus | ESCC | carbohydrate derivative catabolic process | 99/8552 | 172/18723 | 1.11e-03 | 5.54e-03 | 99 |
| GO:00329631 | Esophagus | ESCC | collagen metabolic process | 62/8552 | 104/18723 | 2.90e-03 | 1.22e-02 | 62 |
| GO:001046620 | Esophagus | ESCC | negative regulation of peptidase activity | 140/8552 | 262/18723 | 6.73e-03 | 2.46e-02 | 140 |
| GO:001095119 | Esophagus | ESCC | negative regulation of endopeptidase activity | 135/8552 | 252/18723 | 6.86e-03 | 2.51e-02 | 135 |
| GO:00226172 | Esophagus | ESCC | extracellular matrix disassembly | 39/8552 | 63/18723 | 6.92e-03 | 2.52e-02 | 39 |
| GO:19030532 | Esophagus | ESCC | regulation of extracellular matrix organization | 30/8552 | 48/18723 | 1.40e-02 | 4.57e-02 | 30 |
| GO:0006516 | Esophagus | ESCC | glycoprotein catabolic process | 19/8552 | 28/18723 | 1.49e-02 | 4.84e-02 | 19 |
| GO:004217612 | Liver | Cirrhotic | regulation of protein catabolic process | 181/4634 | 391/18723 | 7.94e-21 | 2.77e-18 | 181 |
| GO:00224117 | Liver | Cirrhotic | cellular component disassembly | 182/4634 | 443/18723 | 1.59e-14 | 1.54e-12 | 182 |
| GO:005254712 | Liver | Cirrhotic | regulation of peptidase activity | 185/4634 | 461/18723 | 1.32e-13 | 1.09e-11 | 185 |
| GO:005254812 | Liver | Cirrhotic | regulation of endopeptidase activity | 172/4634 | 432/18723 | 2.12e-12 | 1.58e-10 | 172 |
| GO:004586112 | Liver | Cirrhotic | negative regulation of proteolysis | 136/4634 | 351/18723 | 3.46e-09 | 1.42e-07 | 136 |
| GO:000989512 | Liver | Cirrhotic | negative regulation of catabolic process | 121/4634 | 320/18723 | 1.21e-07 | 3.39e-06 | 121 |
| GO:005134612 | Liver | Cirrhotic | negative regulation of hydrolase activity | 139/4634 | 379/18723 | 1.24e-07 | 3.42e-06 | 139 |
| GO:001095111 | Liver | Cirrhotic | negative regulation of endopeptidase activity | 98/4634 | 252/18723 | 4.19e-07 | 9.77e-06 | 98 |
| GO:003133012 | Liver | Cirrhotic | negative regulation of cellular catabolic process | 101/4634 | 262/18723 | 4.57e-07 | 1.05e-05 | 101 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa049704 | Breast | IDC | Salivary secretion | 18/867 | 93/8465 | 5.69e-03 | 3.13e-02 | 2.34e-02 | 18 |
| hsa0497011 | Breast | IDC | Salivary secretion | 18/867 | 93/8465 | 5.69e-03 | 3.13e-02 | 2.34e-02 | 18 |
| hsa04970 | Colorectum | FAP | Salivary secretion | 24/1404 | 93/8465 | 1.52e-02 | 4.99e-02 | 3.03e-02 | 24 |
| hsa049701 | Colorectum | FAP | Salivary secretion | 24/1404 | 93/8465 | 1.52e-02 | 4.99e-02 | 3.03e-02 | 24 |
| hsa049702 | Colorectum | CRC | Salivary secretion | 22/1091 | 93/8465 | 3.03e-03 | 1.91e-02 | 1.29e-02 | 22 |
| hsa049703 | Colorectum | CRC | Salivary secretion | 22/1091 | 93/8465 | 3.03e-03 | 1.91e-02 | 1.29e-02 | 22 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| CST3 | SNV | Missense_Mutation | rs759445850 | c.416N>T | p.Ser139Leu | p.S139L | P01034 | protein_coding | tolerated(0.36) | benign(0.001) | TCGA-A8-A06O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | SD |
| CST3 | SNV | Missense_Mutation | novel | c.267N>A | p.Phe89Leu | p.F89L | P01034 | protein_coding | tolerated(0.17) | benign(0.187) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CST3 | SNV | Missense_Mutation | c.169N>T | p.Val57Phe | p.V57F | P01034 | protein_coding | deleterious(0.01) | probably_damaging(0.988) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CST3 | SNV | Missense_Mutation | c.399N>T | p.Gln133His | p.Q133H | P01034 | protein_coding | tolerated(0.13) | benign(0.407) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CST3 | SNV | Missense_Mutation | c.287N>A | p.Arg96Gln | p.R96Q | P01034 | protein_coding | deleterious(0.04) | probably_damaging(0.934) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CST3 | SNV | Missense_Mutation | novel | c.364N>A | p.Phe122Ile | p.F122I | P01034 | protein_coding | tolerated(0.12) | benign(0.043) | TCGA-EY-A547-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CST3 | SNV | Missense_Mutation | c.359A>T | p.Lys120Ile | p.K120I | P01034 | protein_coding | deleterious(0.01) | possibly_damaging(0.626) | TCGA-97-7554-01 | Lung | lung adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | alimta | SD | |
| CST3 | SNV | Missense_Mutation | novel | c.385N>T | p.Ala129Ser | p.A129S | P01034 | protein_coding | tolerated(0.78) | benign(0.011) | TCGA-58-A46M-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| CST3 | SNV | Missense_Mutation | novel | c.326N>A | p.Cys109Tyr | p.C109Y | P01034 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-P3-A5QF-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cetuximab | PD |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| 1471 | CST3 | ENZYME, DRUGGABLE GENOME, PROTEASE INHIBITOR | DIGOXIN | DIGOXIN | 17698593 | |
| 1471 | CST3 | ENZYME, DRUGGABLE GENOME, PROTEASE INHIBITOR | RIBAVIRIN | RIBAVIRIN | 18637076 |
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