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Gene: FANCA |
Gene summary for FANCA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FANCA | Gene ID | 2175 |
| Gene name | FA complementation group A | |
| Gene Alias | FA | |
| Cytomap | 16q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | O15360 |
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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 |
| 2175 | FANCA | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 5.11e-03 | 1.82e-01 | 0.0208 |
| 2175 | FANCA | CCI_1 | Human | Cervix | CC | 1.45e-11 | 6.31e-01 | 0.528 |
| 2175 | FANCA | CCI_2 | Human | Cervix | CC | 9.85e-07 | 4.98e-01 | 0.5249 |
| 2175 | FANCA | CCI_3 | Human | Cervix | CC | 5.99e-10 | 5.98e-01 | 0.516 |
| 2175 | FANCA | CCII_1 | Human | Cervix | CC | 1.80e-03 | 2.37e-01 | 0.3249 |
| 2175 | FANCA | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.06e-02 | 9.45e-01 | 0.3487 |
| 2175 | FANCA | A001-C-119 | Human | Colorectum | FAP | 6.05e-06 | 5.42e-01 | -0.1557 |
| 2175 | FANCA | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 7.76e-03 | 2.05e-01 | -0.1269 |
| 2175 | FANCA | HCC1_Meng | Human | Liver | HCC | 3.81e-09 | 2.18e-02 | 0.0246 |
| 2175 | FANCA | HCC2 | Human | Liver | HCC | 6.36e-04 | 1.91e+00 | 0.5341 |
| 2175 | FANCA | S014 | Human | Liver | HCC | 5.35e-14 | 5.96e-01 | 0.2254 |
| 2175 | FANCA | S015 | Human | Liver | HCC | 8.83e-04 | 2.82e-01 | 0.2375 |
| 2175 | FANCA | S016 | Human | Liver | HCC | 7.99e-10 | 3.32e-01 | 0.2243 |
| 2175 | FANCA | S027 | Human | Liver | HCC | 4.43e-03 | 3.05e-01 | 0.2446 |
| 2175 | FANCA | S028 | Human | Liver | HCC | 1.82e-03 | 2.37e-01 | 0.2503 |
| 2175 | FANCA | S029 | Human | Liver | HCC | 1.90e-03 | 2.07e-01 | 0.2581 |
| 2175 | FANCA | C04 | Human | Oral cavity | OSCC | 5.49e-09 | 3.66e-01 | 0.2633 |
| 2175 | FANCA | C21 | Human | Oral cavity | OSCC | 5.81e-29 | 8.35e-01 | 0.2678 |
| 2175 | FANCA | C30 | Human | Oral cavity | OSCC | 8.26e-09 | 3.52e-01 | 0.3055 |
| 2175 | FANCA | C38 | Human | Oral cavity | OSCC | 9.35e-07 | 4.10e-01 | 0.172 |
| 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 | ||
| 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 | ||
| 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 | ||
| 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 |
| GO:00421108 | Cervix | CC | T cell activation | 107/2311 | 487/18723 | 1.24e-09 | 1.46e-07 | 107 |
| GO:00508638 | Cervix | CC | regulation of T cell activation | 80/2311 | 329/18723 | 1.28e-09 | 1.47e-07 | 80 |
| GO:190370610 | Cervix | CC | regulation of hemopoiesis | 80/2311 | 367/18723 | 2.14e-07 | 9.55e-06 | 80 |
| GO:00614588 | Cervix | CC | reproductive system development | 87/2311 | 427/18723 | 1.37e-06 | 4.55e-05 | 87 |
| GO:00486088 | Cervix | CC | reproductive structure development | 86/2311 | 424/18723 | 1.90e-06 | 5.97e-05 | 86 |
| GO:00510904 | Cervix | CC | regulation of DNA-binding transcription factor activity | 87/2311 | 440/18723 | 4.85e-06 | 1.22e-04 | 87 |
| GO:19021056 | Cervix | CC | regulation of leukocyte differentiation | 61/2311 | 279/18723 | 5.16e-06 | 1.29e-04 | 61 |
| GO:00507273 | Cervix | CC | regulation of inflammatory response | 75/2311 | 386/18723 | 3.95e-05 | 6.18e-04 | 75 |
| GO:0045580 | Cervix | CC | regulation of T cell differentiation | 33/2311 | 146/18723 | 3.75e-04 | 3.87e-03 | 33 |
| GO:00302173 | Cervix | CC | T cell differentiation | 51/2311 | 257/18723 | 3.81e-04 | 3.89e-03 | 51 |
| GO:19031314 | Cervix | CC | mononuclear cell differentiation | 76/2311 | 426/18723 | 5.66e-04 | 5.42e-03 | 76 |
| GO:00456192 | Cervix | CC | regulation of lymphocyte differentiation | 37/2311 | 174/18723 | 6.06e-04 | 5.69e-03 | 37 |
| GO:0045589 | Cervix | CC | regulation of regulatory T cell differentiation | 9/2311 | 28/18723 | 5.02e-03 | 2.98e-02 | 9 |
| GO:00300981 | Cervix | CC | lymphocyte differentiation | 63/2311 | 374/18723 | 6.21e-03 | 3.52e-02 | 63 |
| GO:00482851 | Cervix | CC | organelle fission | 78/2311 | 488/18723 | 9.70e-03 | 4.79e-02 | 78 |
| GO:0045066 | Cervix | CC | regulatory T cell differentiation | 9/2311 | 31/18723 | 1.04e-02 | 4.97e-02 | 9 |
| GO:004211013 | Cervix | HSIL_HPV | T cell activation | 48/737 | 487/18723 | 5.12e-09 | 7.61e-07 | 48 |
| GO:005072711 | Cervix | HSIL_HPV | regulation of inflammatory response | 41/737 | 386/18723 | 8.30e-09 | 1.03e-06 | 41 |
| GO:005086312 | Cervix | HSIL_HPV | regulation of T cell activation | 37/737 | 329/18723 | 9.84e-09 | 1.19e-06 | 37 |
| GO:190370613 | Cervix | HSIL_HPV | regulation of hemopoiesis | 35/737 | 367/18723 | 1.35e-06 | 6.21e-05 | 35 |
| Page: 1 2 3 4 5 |
| 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. |
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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 |
| FANCA | SNV | Missense_Mutation | c.502C>G | p.Gln168Glu | p.Q168E | O15360 | protein_coding | deleterious(0.03) | benign(0.006) | TCGA-A8-A09I-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| FANCA | SNV | Missense_Mutation | c.2791N>C | p.Asp931His | p.D931H | O15360 | protein_coding | deleterious(0) | probably_damaging(0.963) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| FANCA | SNV | Missense_Mutation | c.112N>A | p.Glu38Lys | p.E38K | O15360 | protein_coding | tolerated(0.15) | benign(0.272) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| FANCA | SNV | Missense_Mutation | rs376103033 | c.3157N>T | p.Arg1053Cys | p.R1053C | O15360 | protein_coding | tolerated(0.23) | benign(0.015) | TCGA-AN-A04A-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| FANCA | SNV | Missense_Mutation | rs764206631 | c.3250N>T | p.Arg1084Cys | p.R1084C | O15360 | protein_coding | tolerated(0.07) | benign(0.003) | TCGA-AR-A0TR-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| FANCA | SNV | Missense_Mutation | c.3043G>A | p.Glu1015Lys | p.E1015K | O15360 | protein_coding | tolerated(0.74) | benign(0.003) | TCGA-BH-A1EO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| FANCA | SNV | Missense_Mutation | c.2080N>T | p.Asp694Tyr | p.D694Y | O15360 | protein_coding | tolerated(0.06) | possibly_damaging(0.819) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| FANCA | SNV | Missense_Mutation | c.155N>T | p.Arg52Leu | p.R52L | O15360 | protein_coding | tolerated(0.06) | possibly_damaging(0.468) | TCGA-D8-A1J9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| FANCA | insertion | Nonsense_Mutation | novel | c.3409_3410insTCTTCCATGAGTGTGGGTAATAAAT | p.Gly1137ValfsTer7 | p.G1137Vfs*7 | O15360 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| FANCA | insertion | Nonsense_Mutation | novel | c.3130_3131insTGAGAGTCTGAGCCCTTGGGA | p.Gln1044delinsLeuArgValTerAlaLeuGlyLys | p.Q1044delinsLRV*ALGK | O15360 | protein_coding | TCGA-A2-A0CM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | 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 |
| 2175 | FANCA | CLINICALLY ACTIONABLE, DNA REPAIR | CISPLATIN | CISPLATIN | 26181256 |
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