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Gene: RFWD3 |
Gene summary for RFWD3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RFWD3 | Gene ID | 55159 |
| Gene name | ring finger and WD repeat domain 3 | |
| Gene Alias | FANCW | |
| Cytomap | 16q23.1 | |
| Gene Type | protein-coding | GO ID | GO:0000075 | UniProtAcc | Q6PCD5 |
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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 |
| 55159 | RFWD3 | CCI_1 | Human | Cervix | CC | 5.02e-03 | 4.53e-01 | 0.528 |
| 55159 | RFWD3 | CCI_2 | Human | Cervix | CC | 8.71e-07 | 7.09e-01 | 0.5249 |
| 55159 | RFWD3 | CCI_3 | Human | Cervix | CC | 7.70e-05 | 6.36e-01 | 0.516 |
| 55159 | RFWD3 | HCC1_Meng | Human | Liver | HCC | 6.44e-10 | 3.59e-04 | 0.0246 |
| 55159 | RFWD3 | HCC2_Meng | Human | Liver | HCC | 4.41e-05 | 3.11e-02 | 0.0107 |
| 55159 | RFWD3 | HCC1 | Human | Liver | HCC | 2.15e-07 | 3.19e+00 | 0.5336 |
| 55159 | RFWD3 | HCC2 | Human | Liver | HCC | 1.80e-12 | 2.79e+00 | 0.5341 |
| 55159 | RFWD3 | S028 | Human | Liver | HCC | 9.68e-06 | 3.72e-01 | 0.2503 |
| 55159 | RFWD3 | C04 | Human | Oral cavity | OSCC | 2.03e-10 | 3.82e-01 | 0.2633 |
| 55159 | RFWD3 | C21 | Human | Oral cavity | OSCC | 3.61e-17 | 5.11e-01 | 0.2678 |
| 55159 | RFWD3 | C30 | Human | Oral cavity | OSCC | 3.08e-18 | 7.79e-01 | 0.3055 |
| 55159 | RFWD3 | C38 | Human | Oral cavity | OSCC | 1.30e-04 | 2.43e-01 | 0.172 |
| 55159 | RFWD3 | C43 | Human | Oral cavity | OSCC | 1.08e-05 | 1.75e-01 | 0.1704 |
| 55159 | RFWD3 | C46 | Human | Oral cavity | OSCC | 6.05e-12 | 2.18e-01 | 0.1673 |
| 55159 | RFWD3 | C57 | Human | Oral cavity | OSCC | 3.31e-06 | 2.26e-01 | 0.1679 |
| 55159 | RFWD3 | C08 | Human | Oral cavity | OSCC | 5.46e-04 | 1.47e-01 | 0.1919 |
| 55159 | RFWD3 | LN22 | Human | Oral cavity | OSCC | 2.93e-08 | 3.86e-01 | 0.1733 |
| 55159 | RFWD3 | LN46 | Human | Oral cavity | OSCC | 4.98e-08 | 2.69e-01 | 0.1666 |
| 55159 | RFWD3 | LP15 | Human | Oral cavity | LP | 3.77e-02 | 2.23e-01 | 0.2174 |
| 55159 | RFWD3 | LP17 | Human | Oral cavity | LP | 8.02e-06 | 3.50e-01 | 0.2349 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 |
| ∗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:0000724 | Oral cavity | OSCC | double-strand break repair via homologous recombination | 69/7305 | 138/18723 | 5.52e-03 | 2.14e-02 | 69 |
| GO:19019761 | Oral cavity | OSCC | regulation of cell cycle checkpoint | 20/7305 | 33/18723 | 9.78e-03 | 3.45e-02 | 20 |
| GO:000734614 | Oral cavity | LP | regulation of mitotic cell cycle | 163/4623 | 457/18723 | 7.64e-08 | 2.56e-06 | 163 |
| GO:004477215 | Oral cavity | LP | mitotic cell cycle phase transition | 150/4623 | 424/18723 | 4.38e-07 | 1.23e-05 | 150 |
| GO:001021216 | Oral cavity | LP | response to ionizing radiation | 64/4623 | 148/18723 | 5.60e-07 | 1.51e-05 | 64 |
| GO:000626011 | Oral cavity | LP | DNA replication | 97/4623 | 260/18723 | 3.67e-06 | 7.75e-05 | 97 |
| GO:000931417 | Oral cavity | LP | response to radiation | 155/4623 | 456/18723 | 4.12e-06 | 8.49e-05 | 155 |
| GO:200102018 | Oral cavity | LP | regulation of response to DNA damage stimulus | 82/4623 | 219/18723 | 1.71e-05 | 2.97e-04 | 82 |
| GO:000008213 | Oral cavity | LP | G1/S transition of mitotic cell cycle | 80/4623 | 214/18723 | 2.30e-05 | 3.74e-04 | 80 |
| GO:004484313 | Oral cavity | LP | cell cycle G1/S phase transition | 88/4623 | 241/18723 | 2.62e-05 | 4.21e-04 | 88 |
| GO:190199012 | Oral cavity | LP | regulation of mitotic cell cycle phase transition | 104/4623 | 299/18723 | 5.34e-05 | 7.41e-04 | 104 |
| GO:004578612 | Oral cavity | LP | negative regulation of cell cycle | 127/4623 | 385/18723 | 1.33e-04 | 1.53e-03 | 127 |
| GO:004593012 | Oral cavity | LP | negative regulation of mitotic cell cycle | 83/4623 | 235/18723 | 1.62e-04 | 1.82e-03 | 83 |
| GO:003157115 | Oral cavity | LP | mitotic G1 DNA damage checkpoint | 17/4623 | 30/18723 | 1.81e-04 | 2.01e-03 | 17 |
| GO:004481914 | Oral cavity | LP | mitotic G1/S transition checkpoint | 17/4623 | 31/18723 | 3.09e-04 | 3.15e-03 | 17 |
| GO:190198712 | Oral cavity | LP | regulation of cell cycle phase transition | 126/4623 | 390/18723 | 3.69e-04 | 3.64e-03 | 126 |
| GO:000709311 | Oral cavity | LP | mitotic cell cycle checkpoint | 48/4623 | 129/18723 | 1.03e-03 | 8.67e-03 | 48 |
| GO:190280612 | Oral cavity | LP | regulation of cell cycle G1/S phase transition | 59/4623 | 168/18723 | 1.55e-03 | 1.20e-02 | 59 |
| GO:004277013 | Oral cavity | LP | signal transduction in response to DNA damage | 60/4623 | 172/18723 | 1.71e-03 | 1.31e-02 | 60 |
| GO:190199112 | Oral cavity | LP | negative regulation of mitotic cell cycle phase transition | 62/4623 | 179/18723 | 1.76e-03 | 1.34e-02 | 62 |
| 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 |
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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. |
| 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 |
| RFWD3 | SNV | Missense_Mutation | c.2204N>T | p.Ser735Leu | p.S735L | Q6PCD5 | protein_coding | tolerated(0.06) | benign(0.01) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RFWD3 | SNV | Missense_Mutation | c.1334N>G | p.Ser445Cys | p.S445C | Q6PCD5 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RFWD3 | SNV | Missense_Mutation | c.244N>C | p.Glu82Gln | p.E82Q | Q6PCD5 | protein_coding | deleterious_low_confidence(0.05) | probably_damaging(0.996) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RFWD3 | SNV | Missense_Mutation | c.1219N>G | p.Gln407Glu | p.Q407E | Q6PCD5 | protein_coding | tolerated(0.48) | benign(0.021) | TCGA-D8-A1J9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RFWD3 | SNV | Missense_Mutation | rs747018311 | c.1211N>T | p.Thr404Met | p.T404M | Q6PCD5 | protein_coding | tolerated(0.39) | benign(0) | TCGA-E2-A1B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Adriamycin | SD |
| RFWD3 | insertion | Frame_Shift_Ins | novel | c.178_179insACAGACAGTGCCAGGTAAATAAATATATGGATAAGTCTGTGATCAT | p.Val60AspfsTer35 | p.V60Dfs*35 | Q6PCD5 | protein_coding | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD | ||
| RFWD3 | insertion | Frame_Shift_Ins | novel | c.1227_1228insTA | p.Asn410Ter | p.N410* | Q6PCD5 | protein_coding | TCGA-BH-A0E2-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | ||
| RFWD3 | SNV | Missense_Mutation | novel | c.356N>T | p.Ser119Leu | p.S119L | Q6PCD5 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.994) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD |
| RFWD3 | SNV | Missense_Mutation | novel | c.2198G>A | p.Ser733Asn | p.S733N | Q6PCD5 | protein_coding | tolerated(0.07) | benign(0.037) | TCGA-C5-A8XK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| RFWD3 | insertion | Nonsense_Mutation | novel | c.532_533insAAGCTTCA | p.Leu178Ter | p.L178* | Q6PCD5 | protein_coding | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| Page: 1 2 3 4 5 6 7 |
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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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