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Gene: RFC3 |
Gene summary for RFC3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RFC3 | Gene ID | 5983 |
| Gene name | replication factor C subunit 3 | |
| Gene Alias | RFC38 | |
| Cytomap | 13q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000731 | UniProtAcc | A0A024RDQ8 |
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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 |
| 5983 | RFC3 | P2T-E | Human | Esophagus | ESCC | 1.04e-11 | 3.22e-01 | 0.1177 |
| 5983 | RFC3 | P5T-E | Human | Esophagus | ESCC | 2.72e-10 | 1.64e-01 | 0.1327 |
| 5983 | RFC3 | P8T-E | Human | Esophagus | ESCC | 1.14e-07 | 2.39e-01 | 0.0889 |
| 5983 | RFC3 | P10T-E | Human | Esophagus | ESCC | 2.09e-11 | 2.88e-01 | 0.116 |
| 5983 | RFC3 | P12T-E | Human | Esophagus | ESCC | 1.01e-02 | 7.42e-02 | 0.1122 |
| 5983 | RFC3 | P16T-E | Human | Esophagus | ESCC | 8.66e-05 | 1.24e-01 | 0.1153 |
| 5983 | RFC3 | P21T-E | Human | Esophagus | ESCC | 1.09e-02 | 1.25e-01 | 0.1617 |
| 5983 | RFC3 | P22T-E | Human | Esophagus | ESCC | 9.87e-03 | 7.34e-02 | 0.1236 |
| 5983 | RFC3 | P24T-E | Human | Esophagus | ESCC | 1.67e-05 | 1.64e-01 | 0.1287 |
| 5983 | RFC3 | P26T-E | Human | Esophagus | ESCC | 4.49e-08 | 1.25e-01 | 0.1276 |
| 5983 | RFC3 | P28T-E | Human | Esophagus | ESCC | 1.17e-13 | 1.97e-01 | 0.1149 |
| 5983 | RFC3 | P31T-E | Human | Esophagus | ESCC | 8.74e-11 | 1.90e-01 | 0.1251 |
| 5983 | RFC3 | P32T-E | Human | Esophagus | ESCC | 1.13e-07 | 1.95e-01 | 0.1666 |
| 5983 | RFC3 | P36T-E | Human | Esophagus | ESCC | 2.40e-03 | 1.67e-01 | 0.1187 |
| 5983 | RFC3 | P49T-E | Human | Esophagus | ESCC | 4.04e-03 | 6.12e-01 | 0.1768 |
| 5983 | RFC3 | P52T-E | Human | Esophagus | ESCC | 1.13e-07 | 1.76e-01 | 0.1555 |
| 5983 | RFC3 | P56T-E | Human | Esophagus | ESCC | 3.41e-04 | 5.19e-01 | 0.1613 |
| 5983 | RFC3 | P62T-E | Human | Esophagus | ESCC | 7.81e-03 | 1.44e-01 | 0.1302 |
| 5983 | RFC3 | P65T-E | Human | Esophagus | ESCC | 4.76e-02 | 1.09e-01 | 0.0978 |
| 5983 | RFC3 | P76T-E | Human | Esophagus | ESCC | 2.69e-06 | 2.04e-01 | 0.1207 |
| Page: 1 2 |
| 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 | ||
| 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:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:005105215 | Esophagus | ESCC | regulation of DNA metabolic process | 232/8552 | 359/18723 | 2.40e-13 | 1.13e-11 | 232 |
| GO:007189716 | Esophagus | ESCC | DNA biosynthetic process | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
| GO:005105417 | Esophagus | ESCC | positive regulation of DNA metabolic process | 139/8552 | 201/18723 | 1.20e-11 | 4.33e-10 | 139 |
| GO:200057319 | Esophagus | ESCC | positive regulation of DNA biosynthetic process | 56/8552 | 66/18723 | 4.51e-11 | 1.45e-09 | 56 |
| GO:2000278110 | Esophagus | ESCC | regulation of DNA biosynthetic process | 81/8552 | 106/18723 | 9.81e-11 | 2.96e-09 | 81 |
| GO:00062612 | Esophagus | ESCC | DNA-dependent DNA replication | 100/8552 | 151/18723 | 2.61e-07 | 3.94e-06 | 100 |
| GO:00062754 | Esophagus | ESCC | regulation of DNA replication | 73/8552 | 107/18723 | 1.97e-06 | 2.28e-05 | 73 |
| GO:003239214 | Esophagus | ESCC | DNA geometric change | 62/8552 | 90/18723 | 7.02e-06 | 7.04e-05 | 62 |
| GO:003250813 | Esophagus | ESCC | DNA duplex unwinding | 58/8552 | 84/18723 | 1.23e-05 | 1.14e-04 | 58 |
| GO:0090329 | Esophagus | ESCC | regulation of DNA-dependent DNA replication | 30/8552 | 46/18723 | 5.91e-03 | 2.18e-02 | 30 |
| GO:00062603 | Oral cavity | OSCC | DNA replication | 159/7305 | 260/18723 | 3.25e-13 | 1.59e-11 | 159 |
| GO:005105210 | Oral cavity | OSCC | regulation of DNA metabolic process | 207/7305 | 359/18723 | 4.45e-13 | 2.17e-11 | 207 |
| GO:005105414 | Oral cavity | OSCC | positive regulation of DNA metabolic process | 126/7305 | 201/18723 | 8.12e-12 | 3.01e-10 | 126 |
| GO:00718979 | Oral cavity | OSCC | DNA biosynthetic process | 106/7305 | 180/18723 | 4.86e-08 | 8.95e-07 | 106 |
| GO:00323925 | Oral cavity | OSCC | DNA geometric change | 59/7305 | 90/18723 | 3.03e-07 | 4.63e-06 | 59 |
| GO:200027817 | Oral cavity | OSCC | regulation of DNA biosynthetic process | 67/7305 | 106/18723 | 3.85e-07 | 5.75e-06 | 67 |
| GO:00325083 | Oral cavity | OSCC | DNA duplex unwinding | 55/7305 | 84/18723 | 8.05e-07 | 1.12e-05 | 55 |
| GO:200057316 | Oral cavity | OSCC | positive regulation of DNA biosynthetic process | 44/7305 | 66/18723 | 4.91e-06 | 5.57e-05 | 44 |
| GO:00062611 | Oral cavity | OSCC | DNA-dependent DNA replication | 84/7305 | 151/18723 | 2.46e-05 | 2.30e-04 | 84 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa034204 | Oral cavity | OSCC | Nucleotide excision repair | 49/3704 | 63/8465 | 3.48e-08 | 2.91e-07 | 1.48e-07 | 49 |
| hsa03030 | Oral cavity | OSCC | DNA replication | 31/3704 | 36/8465 | 1.70e-07 | 1.19e-06 | 6.03e-07 | 31 |
| hsa03410 | Oral cavity | OSCC | Base excision repair | 32/3704 | 44/8465 | 9.11e-05 | 3.25e-04 | 1.65e-04 | 32 |
| hsa03430 | Oral cavity | OSCC | Mismatch repair | 19/3704 | 23/8465 | 1.55e-04 | 5.34e-04 | 2.72e-04 | 19 |
| hsa0342011 | Oral cavity | OSCC | Nucleotide excision repair | 49/3704 | 63/8465 | 3.48e-08 | 2.91e-07 | 1.48e-07 | 49 |
| hsa030301 | Oral cavity | OSCC | DNA replication | 31/3704 | 36/8465 | 1.70e-07 | 1.19e-06 | 6.03e-07 | 31 |
| hsa034101 | Oral cavity | OSCC | Base excision repair | 32/3704 | 44/8465 | 9.11e-05 | 3.25e-04 | 1.65e-04 | 32 |
| hsa034301 | Oral cavity | OSCC | Mismatch repair | 19/3704 | 23/8465 | 1.55e-04 | 5.34e-04 | 2.72e-04 | 19 |
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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 |
| RFC3 | SNV | Missense_Mutation | c.912N>G | p.Ile304Met | p.I304M | P40938 | protein_coding | tolerated(1) | benign(0.003) | TCGA-C8-A1HG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RFC3 | SNV | Missense_Mutation | rs758867827 | c.344T>C | p.Val115Ala | p.V115A | P40938 | protein_coding | deleterious(0.02) | benign(0.217) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD |
| RFC3 | SNV | Missense_Mutation | c.109N>T | p.His37Tyr | p.H37Y | P40938 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-IR-A3LH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RFC3 | insertion | Nonsense_Mutation | novel | c.211_212insTGCTCTAGGTAGA | p.His71LeufsTer3 | p.H71Lfs*3 | P40938 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| RFC3 | SNV | Missense_Mutation | rs41553716 | c.583N>A | p.Val195Met | p.V195M | P40938 | protein_coding | deleterious(0.01) | possibly_damaging(0.828) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| RFC3 | SNV | Missense_Mutation | c.943N>T | p.Ala315Ser | p.A315S | P40938 | protein_coding | tolerated(0.1) | probably_damaging(0.997) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR | |
| RFC3 | SNV | Missense_Mutation | c.152G>T | p.Arg51Ile | p.R51I | P40938 | protein_coding | deleterious(0.01) | probably_damaging(0.99) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RFC3 | SNV | Missense_Mutation | rs751166752 | c.824N>A | p.Arg275His | p.R275H | P40938 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RFC3 | SNV | Missense_Mutation | rs761230186 | c.548N>A | p.Arg183His | p.R183H | P40938 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| RFC3 | SNV | Missense_Mutation | novel | c.962N>A | p.Arg321His | p.R321H | P40938 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | 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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