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Gene: RFX2 |
Gene summary for RFX2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RFX2 | Gene ID | 5990 |
| Gene name | regulatory factor X2 | |
| Gene Alias | RFX2 | |
| Cytomap | 19p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P48378 |
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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 |
| 5990 | RFX2 | LZE4T | Human | Esophagus | ESCC | 1.49e-04 | 5.99e-02 | 0.0811 |
| 5990 | RFX2 | LZE24T | Human | Esophagus | ESCC | 7.32e-08 | 3.63e-01 | 0.0596 |
| 5990 | RFX2 | P2T-E | Human | Esophagus | ESCC | 5.13e-17 | 1.30e-01 | 0.1177 |
| 5990 | RFX2 | P4T-E | Human | Esophagus | ESCC | 1.99e-03 | 1.08e-01 | 0.1323 |
| 5990 | RFX2 | P5T-E | Human | Esophagus | ESCC | 2.08e-21 | 1.64e-01 | 0.1327 |
| 5990 | RFX2 | P8T-E | Human | Esophagus | ESCC | 4.84e-17 | 2.45e-01 | 0.0889 |
| 5990 | RFX2 | P9T-E | Human | Esophagus | ESCC | 6.65e-08 | 1.01e-01 | 0.1131 |
| 5990 | RFX2 | P10T-E | Human | Esophagus | ESCC | 4.98e-12 | 2.52e-01 | 0.116 |
| 5990 | RFX2 | P11T-E | Human | Esophagus | ESCC | 2.22e-02 | 9.58e-02 | 0.1426 |
| 5990 | RFX2 | P12T-E | Human | Esophagus | ESCC | 8.90e-14 | 2.11e-01 | 0.1122 |
| 5990 | RFX2 | P15T-E | Human | Esophagus | ESCC | 7.60e-11 | 2.23e-01 | 0.1149 |
| 5990 | RFX2 | P16T-E | Human | Esophagus | ESCC | 2.99e-04 | 3.64e-02 | 0.1153 |
| 5990 | RFX2 | P20T-E | Human | Esophagus | ESCC | 1.16e-06 | 1.68e-01 | 0.1124 |
| 5990 | RFX2 | P21T-E | Human | Esophagus | ESCC | 1.51e-19 | 3.66e-01 | 0.1617 |
| 5990 | RFX2 | P22T-E | Human | Esophagus | ESCC | 9.53e-08 | -9.82e-03 | 0.1236 |
| 5990 | RFX2 | P23T-E | Human | Esophagus | ESCC | 2.37e-11 | 4.33e-01 | 0.108 |
| 5990 | RFX2 | P24T-E | Human | Esophagus | ESCC | 3.80e-09 | 5.44e-02 | 0.1287 |
| 5990 | RFX2 | P26T-E | Human | Esophagus | ESCC | 2.52e-16 | 3.35e-01 | 0.1276 |
| 5990 | RFX2 | P27T-E | Human | Esophagus | ESCC | 2.22e-17 | 1.44e-01 | 0.1055 |
| 5990 | RFX2 | P28T-E | Human | Esophagus | ESCC | 3.82e-09 | 1.68e-01 | 0.1149 |
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| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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 |
| GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
| GO:0060271 | Lung | IAC | cilium assembly | 55/2061 | 337/18723 | 1.84e-03 | 1.88e-02 | 55 |
| GO:0044782 | Lung | IAC | cilium organization | 58/2061 | 368/18723 | 3.15e-03 | 2.75e-02 | 58 |
| GO:0010927 | Lung | IAC | cellular component assembly involved in morphogenesis | 21/2061 | 107/18723 | 5.98e-03 | 4.33e-02 | 21 |
| GO:00109271 | Lung | AIS | cellular component assembly involved in morphogenesis | 20/1849 | 107/18723 | 3.79e-03 | 3.52e-02 | 20 |
| GO:00602711 | Lung | MIAC | cilium assembly | 37/967 | 337/18723 | 1.29e-05 | 9.85e-04 | 37 |
| GO:00447821 | Lung | MIAC | cilium organization | 38/967 | 368/18723 | 3.93e-05 | 2.08e-03 | 38 |
| GO:001605010 | Skin | AK | vesicle organization | 45/1910 | 300/18723 | 5.44e-03 | 3.02e-02 | 45 |
| GO:00109273 | Skin | AK | cellular component assembly involved in morphogenesis | 20/1910 | 107/18723 | 5.45e-03 | 3.02e-02 | 20 |
| GO:001605015 | Skin | cSCC | vesicle organization | 135/4864 | 300/18723 | 5.98e-13 | 3.44e-11 | 135 |
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| 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 |
| RFX2 | TRANS | Cervix | Healthy | GJB2,A2ML1,FAM83G, etc. | 2.70e-01 |  |
| RFX2 | M2MAC | Cervix | CC | ZNF793,CCNJ,RRAS, etc. | 2.35e-01 |  |
| RFX2 | ILC | Colorectum | AD | ARHGAP21,GNA13,FAM107B, etc. | 2.92e-02 |  |
| RFX2 | MON | Colorectum | Healthy | ARHGAP21,GNA13,FAM107B, etc. | 1.14e-01 |  |
| RFX2 | TFH | Colorectum | MSI-H | ARHGAP21,GNA13,FAM107B, etc. | 2.69e-02 |  |
| RFX2 | CD8TEXINT | Colorectum | MSS | ARHGAP21,GNA13,FAM107B, etc. | 5.11e-02 |  |
| RFX2 | CD8TCM | Colorectum | SER | ARHGAP21,GNA13,FAM107B, etc. | 4.78e-02 |  |
| RFX2 | MAIT | Colorectum | SER | ARHGAP21,GNA13,FAM107B, etc. | 1.92e-02 | |
| RFX2 | MSC.SEC | Liver | Healthy | EMP1,NFATC2,AGPAT4, etc. | 5.43e-01 |  |
| RFX2 | CILIA | Lung | AAH | ARFGEF3,MCU,SLC22A23, etc. | 4.81e-01 |  |
| ∗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. |
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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 |
| RFX2 | SNV | Missense_Mutation | c.1494N>C | p.Gln498His | p.Q498H | P48378 | protein_coding | deleterious(0.04) | benign(0.013) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RFX2 | SNV | Missense_Mutation | c.1799N>A | p.Ala600Asp | p.A600D | P48378 | protein_coding | tolerated(0.05) | benign(0) | TCGA-BH-A0BO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RFX2 | insertion | Nonsense_Mutation | novel | c.2155_2156insAGCACCATGTGGGAGGGA | p.Ser719delinsTer | p.S719delins* | P48378 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| RFX2 | insertion | In_Frame_Ins | novel | c.718_719insTGAAATTTCCCAAACAATACTTTTCTTTTTTTGTTTTAGAGC | p.Ser240delinsLeuLysPheProLysGlnTyrPheSerPhePheValLeuGluPro | p.S240delinsLKFPKQYFSFFVLEP | P48378 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| RFX2 | SNV | Missense_Mutation | novel | c.851N>G | p.Asp284Gly | p.D284G | P48378 | protein_coding | deleterious(0) | possibly_damaging(0.829) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RFX2 | SNV | Missense_Mutation | c.187C>T | p.Pro63Ser | p.P63S | P48378 | protein_coding | tolerated(0.2) | benign(0.003) | TCGA-JW-A5VJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | |
| RFX2 | SNV | Missense_Mutation | c.710N>G | p.Asn237Ser | p.N237S | P48378 | protein_coding | deleterious(0.02) | probably_damaging(0.913) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RFX2 | SNV | Missense_Mutation | rs200963067 | c.506N>A | p.Arg169His | p.R169H | P48378 | protein_coding | deleterious(0) | probably_damaging(0.953) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| RFX2 | SNV | Missense_Mutation | c.1280A>C | p.Lys427Thr | p.K427T | P48378 | protein_coding | deleterious(0.01) | benign(0.08) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RFX2 | SNV | Missense_Mutation | c.1424N>A | p.Arg475His | p.R475H | P48378 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
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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 |
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