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Gene: RFWD2 |
Gene summary for RFWD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RFWD2 | Gene ID | 64326 |
| Gene name | COP1 E3 ubiquitin ligase | |
| Gene Alias | CFAP78 | |
| Cytomap | 1q25.1-q25.2 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q8NHY2 |
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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 |
| 64326 | RFWD2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.69e-51 | 8.10e-01 | 0.294 |
| 64326 | RFWD2 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 4.49e-26 | 1.81e+00 | 0.3487 |
| 64326 | RFWD2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.46e-59 | 1.47e+00 | 0.281 |
| 64326 | RFWD2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.28e-38 | 7.98e-01 | 0.3859 |
| 64326 | RFWD2 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.52e-20 | 6.49e-01 | 0.2585 |
| 64326 | RFWD2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.21e-31 | 5.70e-01 | 0.3005 |
| 64326 | RFWD2 | AEH-subject1 | Human | Endometrium | AEH | 4.06e-07 | -1.26e-01 | -0.3059 |
| 64326 | RFWD2 | AEH-subject2 | Human | Endometrium | AEH | 1.04e-05 | -1.26e-01 | -0.2525 |
| 64326 | RFWD2 | AEH-subject3 | Human | Endometrium | AEH | 1.87e-06 | -1.26e-01 | -0.2576 |
| 64326 | RFWD2 | AEH-subject4 | Human | Endometrium | AEH | 8.47e-04 | -1.26e-01 | -0.2657 |
| 64326 | RFWD2 | AEH-subject5 | Human | Endometrium | AEH | 1.87e-06 | -1.26e-01 | -0.2953 |
| 64326 | RFWD2 | EEC-subject1 | Human | Endometrium | EEC | 8.53e-06 | -1.26e-01 | -0.2682 |
| 64326 | RFWD2 | EEC-subject2 | Human | Endometrium | EEC | 1.88e-08 | -1.26e-01 | -0.2607 |
| 64326 | RFWD2 | EEC-subject3 | Human | Endometrium | EEC | 3.99e-06 | -1.26e-01 | -0.2525 |
| 64326 | RFWD2 | EEC-subject4 | Human | Endometrium | EEC | 8.71e-07 | -1.26e-01 | -0.2571 |
| 64326 | RFWD2 | EEC-subject5 | Human | Endometrium | EEC | 1.89e-07 | -1.26e-01 | -0.249 |
| 64326 | RFWD2 | GSM5276934 | Human | Endometrium | EEC | 3.99e-06 | -1.26e-01 | -0.0913 |
| 64326 | RFWD2 | GSM5276935 | Human | Endometrium | EEC | 8.77e-08 | -1.26e-01 | -0.123 |
| 64326 | RFWD2 | GSM5276937 | Human | Endometrium | EEC | 3.33e-05 | -1.26e-01 | -0.0897 |
| 64326 | RFWD2 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 3.59e-04 | -1.26e-01 | -0.1869 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0412014 | Cervix | CC | Ubiquitin mediated proteolysis | 49/1267 | 142/8465 | 4.26e-09 | 7.68e-08 | 4.54e-08 | 49 |
| hsa0412015 | Cervix | CC | Ubiquitin mediated proteolysis | 49/1267 | 142/8465 | 4.26e-09 | 7.68e-08 | 4.54e-08 | 49 |
| hsa04120 | Colorectum | AD | Ubiquitin mediated proteolysis | 58/2092 | 142/8465 | 1.46e-05 | 1.53e-04 | 9.76e-05 | 58 |
| hsa041201 | Colorectum | AD | Ubiquitin mediated proteolysis | 58/2092 | 142/8465 | 1.46e-05 | 1.53e-04 | 9.76e-05 | 58 |
| hsa041202 | Colorectum | SER | Ubiquitin mediated proteolysis | 39/1580 | 142/8465 | 6.18e-03 | 3.66e-02 | 2.66e-02 | 39 |
| hsa041203 | Colorectum | SER | Ubiquitin mediated proteolysis | 39/1580 | 142/8465 | 6.18e-03 | 3.66e-02 | 2.66e-02 | 39 |
| hsa041204 | Colorectum | MSS | Ubiquitin mediated proteolysis | 55/1875 | 142/8465 | 5.02e-06 | 6.00e-05 | 3.68e-05 | 55 |
| hsa041205 | Colorectum | MSS | Ubiquitin mediated proteolysis | 55/1875 | 142/8465 | 5.02e-06 | 6.00e-05 | 3.68e-05 | 55 |
| hsa041206 | Colorectum | FAP | Ubiquitin mediated proteolysis | 51/1404 | 142/8465 | 1.55e-08 | 5.84e-07 | 3.55e-07 | 51 |
| hsa041207 | Colorectum | FAP | Ubiquitin mediated proteolysis | 51/1404 | 142/8465 | 1.55e-08 | 5.84e-07 | 3.55e-07 | 51 |
| hsa0412016 | Endometrium | AEH | Ubiquitin mediated proteolysis | 41/1197 | 142/8465 | 3.42e-06 | 4.27e-05 | 3.13e-05 | 41 |
| hsa0412017 | Endometrium | AEH | Ubiquitin mediated proteolysis | 41/1197 | 142/8465 | 3.42e-06 | 4.27e-05 | 3.13e-05 | 41 |
| hsa0412023 | Endometrium | EEC | Ubiquitin mediated proteolysis | 41/1237 | 142/8465 | 7.86e-06 | 9.58e-05 | 7.14e-05 | 41 |
| hsa0412033 | Endometrium | EEC | Ubiquitin mediated proteolysis | 41/1237 | 142/8465 | 7.86e-06 | 9.58e-05 | 7.14e-05 | 41 |
| hsa0412010 | Liver | NAFLD | Ubiquitin mediated proteolysis | 44/1043 | 142/8465 | 2.59e-09 | 1.70e-07 | 1.37e-07 | 44 |
| hsa0412011 | Liver | NAFLD | Ubiquitin mediated proteolysis | 44/1043 | 142/8465 | 2.59e-09 | 1.70e-07 | 1.37e-07 | 44 |
| hsa0412021 | Liver | Cirrhotic | Ubiquitin mediated proteolysis | 72/2530 | 142/8465 | 1.32e-07 | 1.97e-06 | 1.21e-06 | 72 |
| hsa0412031 | Liver | Cirrhotic | Ubiquitin mediated proteolysis | 72/2530 | 142/8465 | 1.32e-07 | 1.97e-06 | 1.21e-06 | 72 |
| hsa0412041 | Liver | HCC | Ubiquitin mediated proteolysis | 110/4020 | 142/8465 | 1.67e-13 | 3.74e-12 | 2.08e-12 | 110 |
| hsa041156 | Liver | HCC | p53 signaling pathway | 46/4020 | 74/8465 | 7.64e-03 | 2.08e-02 | 1.16e-02 | 46 |
| Page: 1 2 |
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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 |
| RFWD2 | SNV | Missense_Mutation | novel | c.1537N>C | p.Glu513Gln | p.E513Q | Q8NHY2 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| RFWD2 | SNV | Missense_Mutation | novel | c.1011N>A | p.Phe337Leu | p.F337L | Q8NHY2 | protein_coding | tolerated(0.33) | possibly_damaging(0.827) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| RFWD2 | SNV | Missense_Mutation | rs753910989 | c.660G>C | p.Gln220His | p.Q220H | Q8NHY2 | protein_coding | tolerated(0.07) | probably_damaging(0.965) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| RFWD2 | SNV | Missense_Mutation | c.1412N>T | p.Ser471Leu | p.S471L | Q8NHY2 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-E2-A1IL-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RFWD2 | insertion | In_Frame_Ins | novel | c.477_478insGAGAAAGAGTCCATGGGTCTCGGGAACTCAGGTTTGTTG | p.Cys159_Ile160insGluLysGluSerMetGlyLeuGlyAsnSerGlyLeuLeu | p.C159_I160insEKESMGLGNSGLL | Q8NHY2 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| RFWD2 | insertion | In_Frame_Ins | novel | c.1325_1326insTGTAAG | p.Thr442_Lys443insValArg | p.T442_K443insVR | Q8NHY2 | protein_coding | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| RFWD2 | insertion | Frame_Shift_Ins | novel | c.1324_1325insT | p.Thr442IlefsTer5 | p.T442Ifs*5 | Q8NHY2 | protein_coding | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| RFWD2 | SNV | Missense_Mutation | novel | c.1846G>A | p.Ala616Thr | p.A616T | Q8NHY2 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-C5-A3HE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| RFWD2 | SNV | Missense_Mutation | c.1625C>G | p.Ser542Cys | p.S542C | Q8NHY2 | protein_coding | tolerated(0.49) | probably_damaging(0.995) | TCGA-IR-A3LF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RFWD2 | SNV | Missense_Mutation | novel | c.1636N>C | p.Asp546His | p.D546H | Q8NHY2 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 |
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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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