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Gene: AFF4 |
Gene summary for AFF4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | AFF4 | Gene ID | 27125 |
| Gene name | AF4/FMR2 family member 4 | |
| Gene Alias | AF5Q31 | |
| Cytomap | 5q31.1 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q9UHB7 |
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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 |
| 27125 | AFF4 | CA_HPV_3 | Human | Cervix | CC | 5.69e-03 | 1.67e-02 | 0.0414 |
| 27125 | AFF4 | CCI_2 | Human | Cervix | CC | 5.34e-11 | 1.07e+00 | 0.5249 |
| 27125 | AFF4 | CCI_3 | Human | Cervix | CC | 3.29e-03 | 5.47e-01 | 0.516 |
| 27125 | AFF4 | L1 | Human | Cervix | CC | 1.59e-04 | -3.27e-01 | 0.0802 |
| 27125 | AFF4 | AEH-subject1 | Human | Endometrium | AEH | 4.67e-36 | 6.84e-01 | -0.3059 |
| 27125 | AFF4 | AEH-subject2 | Human | Endometrium | AEH | 9.53e-13 | 3.37e-01 | -0.2525 |
| 27125 | AFF4 | AEH-subject3 | Human | Endometrium | AEH | 1.31e-09 | 3.29e-01 | -0.2576 |
| 27125 | AFF4 | AEH-subject4 | Human | Endometrium | AEH | 8.88e-26 | 6.26e-01 | -0.2657 |
| 27125 | AFF4 | AEH-subject5 | Human | Endometrium | AEH | 7.99e-12 | 4.19e-01 | -0.2953 |
| 27125 | AFF4 | EEC-subject1 | Human | Endometrium | EEC | 1.68e-25 | 5.78e-01 | -0.2682 |
| 27125 | AFF4 | EEC-subject2 | Human | Endometrium | EEC | 7.65e-15 | 4.36e-01 | -0.2607 |
| 27125 | AFF4 | EEC-subject3 | Human | Endometrium | EEC | 1.22e-17 | 1.63e-01 | -0.2525 |
| 27125 | AFF4 | EEC-subject4 | Human | Endometrium | EEC | 4.11e-09 | 2.92e-01 | -0.2571 |
| 27125 | AFF4 | EEC-subject5 | Human | Endometrium | EEC | 2.11e-12 | 4.16e-01 | -0.249 |
| 27125 | AFF4 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 1.26e-22 | -4.73e-02 | -0.1869 |
| 27125 | AFF4 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 5.93e-15 | -3.36e-02 | -0.1875 |
| 27125 | AFF4 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 9.66e-18 | -1.37e-01 | -0.1883 |
| 27125 | AFF4 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 8.51e-17 | -1.64e-01 | -0.1934 |
| 27125 | AFF4 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 1.84e-28 | -5.56e-02 | -0.1917 |
| 27125 | AFF4 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 3.33e-26 | -1.58e-02 | -0.1916 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa032502 | Liver | HCC | Viral life cycle - HIV-1 | 46/4020 | 63/8465 | 3.25e-05 | 1.88e-04 | 1.04e-04 | 46 |
| hsa0325011 | Liver | HCC | Viral life cycle - HIV-1 | 46/4020 | 63/8465 | 3.25e-05 | 1.88e-04 | 1.04e-04 | 46 |
| hsa032504 | Prostate | BPH | Viral life cycle - HIV-1 | 24/1718 | 63/8465 | 8.32e-04 | 3.98e-03 | 2.46e-03 | 24 |
| hsa0325012 | Prostate | BPH | Viral life cycle - HIV-1 | 24/1718 | 63/8465 | 8.32e-04 | 3.98e-03 | 2.46e-03 | 24 |
| 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 |
| AFF4 | SNV | Missense_Mutation | c.1456N>A | p.Val486Met | p.V486M | Q9UHB7 | protein_coding | tolerated(0.26) | probably_damaging(0.992) | TCGA-A7-A0CD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| AFF4 | SNV | Missense_Mutation | c.2491N>G | p.Arg831Gly | p.R831G | Q9UHB7 | protein_coding | deleterious(0.05) | possibly_damaging(0.65) | TCGA-A7-A13D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| AFF4 | SNV | Missense_Mutation | c.2696N>G | p.Ser899Cys | p.S899C | Q9UHB7 | protein_coding | deleterious(0.04) | possibly_damaging(0.845) | TCGA-A8-A09G-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| AFF4 | SNV | Missense_Mutation | rs769422062 | c.2552N>T | p.Thr851Met | p.T851M | Q9UHB7 | protein_coding | tolerated(0.11) | benign(0.278) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| AFF4 | SNV | Missense_Mutation | rs786205680 | c.772N>T | p.Arg258Trp | p.R258W | Q9UHB7 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AR-A0TZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | Doxorubicin | PD |
| AFF4 | SNV | Missense_Mutation | novel | c.1255N>A | p.Glu419Lys | p.E419K | Q9UHB7 | protein_coding | tolerated(0.26) | probably_damaging(0.992) | TCGA-D8-A73U-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| AFF4 | insertion | Nonsense_Mutation | novel | c.1257_1258insATATATTCAGACAAATTAGAATAATACATGACT | p.Glu419_Gly420insIleTyrSerAspLysLeuGluTerTyrMetThr | p.E419_G420insIYSDKLE*YMT | Q9UHB7 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| AFF4 | insertion | Nonsense_Mutation | novel | c.1470_1471insATAAGGTATTCAGACATTTAAAATAT | p.Ser491IlefsTer7 | p.S491Ifs*7 | Q9UHB7 | protein_coding | TCGA-A8-A09B-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | SD | ||
| AFF4 | insertion | Nonsense_Mutation | novel | c.317_318insGGGCTTGGCACTTGGCCTTTAGTTAATAGGTGCTCAGT | p.Ser106ArgfsTer8 | p.S106Rfs*8 | Q9UHB7 | protein_coding | TCGA-AO-A03T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | ||
| AFF4 | insertion | Frame_Shift_Ins | novel | c.371_372insA | p.Ser125LeufsTer8 | p.S125Lfs*8 | Q9UHB7 | protein_coding | TCGA-LQ-A4E4-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
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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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