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Gene: CRTAP |
Gene summary for CRTAP |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CRTAP | Gene ID | 10491 |
| Gene name | cartilage associated protein | |
| Gene Alias | CASP | |
| Cytomap | 3p22.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | O75718 |
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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 |
| 10491 | CRTAP | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.23e-13 | 4.89e-01 | 0.0155 |
| 10491 | CRTAP | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.88e-03 | 3.73e-01 | -0.1808 |
| 10491 | CRTAP | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.46e-11 | 7.07e-01 | -0.0811 |
| 10491 | CRTAP | HTA11_78_2000001011 | Human | Colorectum | AD | 7.97e-10 | 4.90e-01 | -0.1088 |
| 10491 | CRTAP | HTA11_347_2000001011 | Human | Colorectum | AD | 1.11e-17 | 5.22e-01 | -0.1954 |
| 10491 | CRTAP | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.09e-03 | 4.41e-01 | -0.1207 |
| 10491 | CRTAP | HTA11_696_2000001011 | Human | Colorectum | AD | 1.39e-12 | 4.76e-01 | -0.1464 |
| 10491 | CRTAP | HTA11_866_2000001011 | Human | Colorectum | AD | 3.19e-02 | 2.65e-01 | -0.1001 |
| 10491 | CRTAP | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.25e-17 | 7.94e-01 | -0.059 |
| 10491 | CRTAP | HTA11_546_2000001011 | Human | Colorectum | AD | 2.71e-02 | 3.91e-01 | -0.0842 |
| 10491 | CRTAP | HTA11_7862_2000001011 | Human | Colorectum | AD | 1.01e-05 | 5.01e-01 | -0.0179 |
| 10491 | CRTAP | HTA11_866_3004761011 | Human | Colorectum | AD | 1.08e-18 | 7.13e-01 | 0.096 |
| 10491 | CRTAP | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.72e-04 | 6.18e-01 | 0.0446 |
| 10491 | CRTAP | HTA11_8622_2000001021 | Human | Colorectum | SER | 6.69e-04 | 4.85e-01 | 0.0528 |
| 10491 | CRTAP | HTA11_7663_2000001011 | Human | Colorectum | SER | 2.72e-03 | 5.07e-01 | 0.0131 |
| 10491 | CRTAP | HTA11_10623_2000001011 | Human | Colorectum | AD | 1.13e-07 | 5.79e-01 | -0.0177 |
| 10491 | CRTAP | HTA11_6801_2000001011 | Human | Colorectum | SER | 4.94e-04 | 6.19e-01 | 0.0171 |
| 10491 | CRTAP | HTA11_10711_2000001011 | Human | Colorectum | AD | 9.43e-04 | 3.52e-01 | 0.0338 |
| 10491 | CRTAP | HTA11_7696_3000711011 | Human | Colorectum | AD | 5.56e-26 | 7.52e-01 | 0.0674 |
| 10491 | CRTAP | HTA11_6818_2000001011 | Human | Colorectum | AD | 1.68e-05 | 5.76e-01 | 0.0112 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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:00452293 | Oral cavity | OSCC | external encapsulating structure organization | 147/7305 | 304/18723 | 5.30e-04 | 3.08e-03 | 147 |
| GO:00430623 | Oral cavity | OSCC | extracellular structure organization | 146/7305 | 302/18723 | 5.59e-04 | 3.23e-03 | 146 |
| GO:000645719 | Oral cavity | LP | protein folding | 125/4623 | 212/18723 | 1.62e-26 | 8.45e-24 | 125 |
| GO:0031647110 | Oral cavity | LP | regulation of protein stability | 132/4623 | 298/18723 | 8.16e-14 | 7.99e-12 | 132 |
| GO:006107719 | Oral cavity | LP | chaperone-mediated protein folding | 45/4623 | 67/18723 | 2.58e-13 | 2.41e-11 | 45 |
| GO:0050821110 | Oral cavity | LP | protein stabilization | 88/4623 | 191/18723 | 9.15e-11 | 5.51e-09 | 88 |
| GO:001820815 | Oral cavity | LP | peptidyl-proline modification | 28/4623 | 58/18723 | 8.35e-05 | 1.07e-03 | 28 |
| GO:001812611 | Oral cavity | LP | protein hydroxylation | 14/4623 | 27/18723 | 2.14e-03 | 1.57e-02 | 14 |
| GO:003164726 | Oral cavity | EOLP | regulation of protein stability | 75/2218 | 298/18723 | 1.22e-10 | 1.35e-08 | 75 |
| GO:000645725 | Oral cavity | EOLP | protein folding | 59/2218 | 212/18723 | 1.76e-10 | 1.79e-08 | 59 |
| GO:006107724 | Oral cavity | EOLP | chaperone-mediated protein folding | 28/2218 | 67/18723 | 5.43e-10 | 4.31e-08 | 28 |
| GO:005082126 | Oral cavity | EOLP | protein stabilization | 51/2218 | 191/18723 | 1.37e-08 | 6.40e-07 | 51 |
| GO:003019811 | Oral cavity | EOLP | extracellular matrix organization | 52/2218 | 301/18723 | 3.29e-03 | 1.90e-02 | 52 |
| GO:004306211 | Oral cavity | EOLP | extracellular structure organization | 52/2218 | 302/18723 | 3.52e-03 | 2.01e-02 | 52 |
| GO:004522911 | Oral cavity | EOLP | external encapsulating structure organization | 52/2218 | 304/18723 | 4.04e-03 | 2.23e-02 | 52 |
| GO:003164718 | Prostate | BPH | regulation of protein stability | 111/3107 | 298/18723 | 4.58e-18 | 1.42e-15 | 111 |
| GO:000645716 | Prostate | BPH | protein folding | 85/3107 | 212/18723 | 2.37e-16 | 4.74e-14 | 85 |
| GO:005082118 | Prostate | BPH | protein stabilization | 75/3107 | 191/18723 | 4.96e-14 | 5.68e-12 | 75 |
| GO:006107716 | Prostate | BPH | chaperone-mediated protein folding | 30/3107 | 67/18723 | 5.88e-08 | 1.57e-06 | 30 |
| GO:00182087 | Prostate | BPH | peptidyl-proline modification | 18/3107 | 58/18723 | 4.75e-03 | 2.27e-02 | 18 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| CRTAP | SNV | Missense_Mutation | rs766089362 | c.1144N>A | p.Asp382Asn | p.D382N | O75718 | protein_coding | tolerated(0.05) | benign(0.015) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| CRTAP | SNV | Missense_Mutation | rs142090883 | c.514N>G | p.Leu172Val | p.L172V | O75718 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| CRTAP | SNV | Missense_Mutation | c.1094N>T | p.Thr365Ile | p.T365I | O75718 | protein_coding | deleterious(0.02) | probably_damaging(0.996) | TCGA-E2-A15K-06 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| CRTAP | insertion | Frame_Shift_Ins | novel | c.1016_1017insTAATATGAACTTTATTATTTTAGCCATTGTTCAAT | p.Gln339HisfsTer38 | p.Q339Hfs*38 | O75718 | protein_coding | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| CRTAP | insertion | Frame_Shift_Ins | novel | c.516_517insAATAACCACCTTCTTAAACTTTCCTCCAATTACC | p.Leu173AsnfsTer16 | p.L173Nfs*16 | O75718 | protein_coding | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| CRTAP | SNV | Missense_Mutation | rs149281572 | c.643N>T | p.Arg215Trp | p.R215W | O75718 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD |
| CRTAP | SNV | Missense_Mutation | c.1073N>A | p.Ala358Glu | p.A358E | O75718 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-3833-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CRTAP | SNV | Missense_Mutation | rs145644749 | c.733N>A | p.Ala245Thr | p.A245T | O75718 | protein_coding | deleterious(0.03) | probably_damaging(0.996) | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR |
| CRTAP | SNV | Missense_Mutation | c.1188A>T | p.Glu396Asp | p.E396D | O75718 | protein_coding | tolerated_low_confidence(0.3) | benign(0) | TCGA-NH-A6GC-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | SD | |
| CRTAP | SNV | Missense_Mutation | novel | c.899A>G | p.Tyr300Cys | p.Y300C | O75718 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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 |
| Page: 1 |
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