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Gene: CEP290 |
Gene summary for CEP290 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CEP290 | Gene ID | 80184 |
| Gene name | centrosomal protein 290 | |
| Gene Alias | 3H11Ag | |
| Cytomap | 12q21.32 | |
| Gene Type | protein-coding | GO ID | GO:0001654 | UniProtAcc | O15078 |
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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 |
| 80184 | CEP290 | LZE4T | Human | Esophagus | ESCC | 2.76e-08 | 2.95e-01 | 0.0811 |
| 80184 | CEP290 | LZE5T | Human | Esophagus | ESCC | 4.73e-05 | 3.13e-01 | 0.0514 |
| 80184 | CEP290 | LZE7T | Human | Esophagus | ESCC | 8.63e-08 | 3.18e-01 | 0.0667 |
| 80184 | CEP290 | LZE8T | Human | Esophagus | ESCC | 5.30e-04 | 1.62e-01 | 0.067 |
| 80184 | CEP290 | LZE24T | Human | Esophagus | ESCC | 6.21e-10 | 2.80e-01 | 0.0596 |
| 80184 | CEP290 | P1T-E | Human | Esophagus | ESCC | 2.10e-14 | 4.91e-01 | 0.0875 |
| 80184 | CEP290 | P2T-E | Human | Esophagus | ESCC | 5.93e-47 | 1.05e+00 | 0.1177 |
| 80184 | CEP290 | P4T-E | Human | Esophagus | ESCC | 6.21e-25 | 5.21e-01 | 0.1323 |
| 80184 | CEP290 | P5T-E | Human | Esophagus | ESCC | 4.63e-21 | 4.46e-01 | 0.1327 |
| 80184 | CEP290 | P8T-E | Human | Esophagus | ESCC | 5.99e-25 | 4.24e-01 | 0.0889 |
| 80184 | CEP290 | P9T-E | Human | Esophagus | ESCC | 2.13e-12 | 2.22e-01 | 0.1131 |
| 80184 | CEP290 | P10T-E | Human | Esophagus | ESCC | 2.44e-21 | 4.36e-01 | 0.116 |
| 80184 | CEP290 | P11T-E | Human | Esophagus | ESCC | 3.09e-10 | 3.79e-01 | 0.1426 |
| 80184 | CEP290 | P12T-E | Human | Esophagus | ESCC | 1.17e-21 | 4.28e-01 | 0.1122 |
| 80184 | CEP290 | P15T-E | Human | Esophagus | ESCC | 1.54e-13 | 3.37e-01 | 0.1149 |
| 80184 | CEP290 | P16T-E | Human | Esophagus | ESCC | 3.30e-34 | 5.35e-01 | 0.1153 |
| 80184 | CEP290 | P17T-E | Human | Esophagus | ESCC | 2.40e-08 | 3.79e-01 | 0.1278 |
| 80184 | CEP290 | P19T-E | Human | Esophagus | ESCC | 2.65e-04 | 5.74e-01 | 0.1662 |
| 80184 | CEP290 | P20T-E | Human | Esophagus | ESCC | 3.35e-15 | 3.14e-01 | 0.1124 |
| 80184 | CEP290 | P21T-E | Human | Esophagus | ESCC | 1.88e-21 | 4.86e-01 | 0.1617 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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:003238618 | Esophagus | ESCC | regulation of intracellular transport | 243/8552 | 337/18723 | 3.20e-23 | 7.25e-21 | 243 |
| GO:0033157110 | Esophagus | ESCC | regulation of intracellular protein transport | 169/8552 | 229/18723 | 3.31e-18 | 3.23e-16 | 169 |
| GO:0032388110 | Esophagus | ESCC | positive regulation of intracellular transport | 152/8552 | 202/18723 | 7.89e-18 | 7.36e-16 | 152 |
| GO:1904951111 | Esophagus | ESCC | positive regulation of establishment of protein localization | 216/8552 | 319/18723 | 1.01e-15 | 6.86e-14 | 216 |
| GO:009031617 | Esophagus | ESCC | positive regulation of intracellular protein transport | 122/8552 | 160/18723 | 2.45e-15 | 1.49e-13 | 122 |
| GO:0051222111 | Esophagus | ESCC | positive regulation of protein transport | 204/8552 | 303/18723 | 1.56e-14 | 8.38e-13 | 204 |
| GO:00224069 | Esophagus | ESCC | membrane docking | 62/8552 | 86/18723 | 5.93e-07 | 7.79e-06 | 62 |
| GO:003514815 | Esophagus | ESCC | tube formation | 96/8552 | 148/18723 | 1.86e-06 | 2.16e-05 | 96 |
| GO:00721759 | Esophagus | ESCC | epithelial tube formation | 86/8552 | 132/18723 | 4.81e-06 | 5.10e-05 | 86 |
| GO:006056210 | Esophagus | ESCC | epithelial tube morphogenesis | 187/8552 | 325/18723 | 9.95e-06 | 9.44e-05 | 187 |
| GO:01400567 | Esophagus | ESCC | organelle localization by membrane tethering | 53/8552 | 77/18723 | 3.33e-05 | 2.74e-04 | 53 |
| GO:00485687 | Esophagus | ESCC | embryonic organ development | 228/8552 | 427/18723 | 7.28e-04 | 3.79e-03 | 228 |
| GO:19055153 | Esophagus | ESCC | non-motile cilium assembly | 39/8552 | 61/18723 | 3.08e-03 | 1.28e-02 | 39 |
| GO:00016559 | Esophagus | ESCC | urogenital system development | 177/8552 | 338/18723 | 7.51e-03 | 2.69e-02 | 177 |
| GO:003238621 | Liver | HCC | regulation of intracellular transport | 231/7958 | 337/18723 | 1.99e-22 | 3.40e-20 | 231 |
| GO:003315721 | Liver | HCC | regulation of intracellular protein transport | 165/7958 | 229/18723 | 8.37e-20 | 1.15e-17 | 165 |
| GO:003238821 | Liver | HCC | positive regulation of intracellular transport | 148/7958 | 202/18723 | 5.15e-19 | 6.66e-17 | 148 |
| GO:009031621 | Liver | HCC | positive regulation of intracellular protein transport | 121/7958 | 160/18723 | 1.27e-17 | 1.39e-15 | 121 |
| GO:190495122 | Liver | HCC | positive regulation of establishment of protein localization | 207/7958 | 319/18723 | 3.95e-16 | 3.29e-14 | 207 |
| GO:005122222 | Liver | HCC | positive regulation of protein transport | 194/7958 | 303/18723 | 2.41e-14 | 1.56e-12 | 194 |
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| 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 |
| CEP290 | SNV | Missense_Mutation | c.5234G>A | p.Ser1745Asn | p.S1745N | O15078 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A1-A0SG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | ||
| CEP290 | SNV | Missense_Mutation | rs376425111 | c.4063C>T | p.Arg1355Cys | p.R1355C | O15078 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-A2-A0YG-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD |
| CEP290 | SNV | Missense_Mutation | c.1475N>G | p.Lys492Arg | p.K492R | O15078 | protein_coding | tolerated(0.27) | benign(0.189) | TCGA-A7-A0DA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| CEP290 | SNV | Missense_Mutation | c.1241N>T | p.Asp414Val | p.D414V | O15078 | protein_coding | deleterious(0.03) | benign(0.026) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CEP290 | SNV | Missense_Mutation | rs565584005 | c.4111N>A | p.Glu1371Lys | p.E1371K | O15078 | protein_coding | deleterious(0.03) | possibly_damaging(0.67) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CEP290 | SNV | Missense_Mutation | novel | c.2397N>T | p.Lys799Asn | p.K799N | O15078 | protein_coding | tolerated(0.09) | benign(0.006) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CEP290 | SNV | Missense_Mutation | novel | c.1859N>G | p.Glu620Gly | p.E620G | O15078 | protein_coding | deleterious(0.01) | possibly_damaging(0.856) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CEP290 | SNV | Missense_Mutation | c.1805T>C | p.Met602Thr | p.M602T | O15078 | protein_coding | tolerated(0.21) | benign(0.007) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| CEP290 | SNV | Missense_Mutation | c.7420G>A | p.Val2474Ile | p.V2474I | O15078 | protein_coding | tolerated_low_confidence(0.44) | benign(0) | TCGA-AQ-A04H-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD | |
| CEP290 | SNV | Missense_Mutation | c.2338N>G | p.Gln780Glu | p.Q780E | O15078 | protein_coding | deleterious(0.01) | benign(0.174) | TCGA-AR-A24V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 |
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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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