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Gene: ABCF3 |
Gene summary for ABCF3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ABCF3 | Gene ID | 55324 |
| Gene name | ATP binding cassette subfamily F member 3 | |
| Gene Alias | EST201864 | |
| Cytomap | 3q27.1 | |
| Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | A0A0S2Z5L1 |
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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 |
| 55324 | ABCF3 | LZE2T | Human | Esophagus | ESCC | 6.89e-03 | 5.23e-01 | 0.082 |
| 55324 | ABCF3 | LZE4T | Human | Esophagus | ESCC | 8.67e-12 | 5.07e-01 | 0.0811 |
| 55324 | ABCF3 | LZE7T | Human | Esophagus | ESCC | 3.96e-08 | 3.61e-01 | 0.0667 |
| 55324 | ABCF3 | LZE8T | Human | Esophagus | ESCC | 7.99e-08 | 2.11e-01 | 0.067 |
| 55324 | ABCF3 | LZE20T | Human | Esophagus | ESCC | 3.02e-06 | 3.51e-01 | 0.0662 |
| 55324 | ABCF3 | LZE22T | Human | Esophagus | ESCC | 2.16e-05 | 4.53e-01 | 0.068 |
| 55324 | ABCF3 | LZE24T | Human | Esophagus | ESCC | 5.65e-10 | 3.53e-01 | 0.0596 |
| 55324 | ABCF3 | LZE21T | Human | Esophagus | ESCC | 4.84e-04 | 5.18e-01 | 0.0655 |
| 55324 | ABCF3 | LZE6T | Human | Esophagus | ESCC | 1.51e-07 | 2.98e-01 | 0.0845 |
| 55324 | ABCF3 | P1T-E | Human | Esophagus | ESCC | 2.12e-09 | 5.29e-01 | 0.0875 |
| 55324 | ABCF3 | P2T-E | Human | Esophagus | ESCC | 5.26e-37 | 6.75e-01 | 0.1177 |
| 55324 | ABCF3 | P4T-E | Human | Esophagus | ESCC | 9.87e-26 | 6.52e-01 | 0.1323 |
| 55324 | ABCF3 | P5T-E | Human | Esophagus | ESCC | 2.23e-19 | 3.32e-01 | 0.1327 |
| 55324 | ABCF3 | P8T-E | Human | Esophagus | ESCC | 9.41e-32 | 5.79e-01 | 0.0889 |
| 55324 | ABCF3 | P9T-E | Human | Esophagus | ESCC | 2.84e-13 | 3.88e-01 | 0.1131 |
| 55324 | ABCF3 | P10T-E | Human | Esophagus | ESCC | 1.52e-19 | 3.56e-01 | 0.116 |
| 55324 | ABCF3 | P11T-E | Human | Esophagus | ESCC | 5.64e-11 | 6.82e-01 | 0.1426 |
| 55324 | ABCF3 | P12T-E | Human | Esophagus | ESCC | 2.72e-21 | 4.77e-01 | 0.1122 |
| 55324 | ABCF3 | P15T-E | Human | Esophagus | ESCC | 1.56e-31 | 7.56e-01 | 0.1149 |
| 55324 | ABCF3 | P16T-E | Human | Esophagus | ESCC | 2.49e-28 | 4.59e-01 | 0.1153 |
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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 | ||
| 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 | ||
| 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:000961518 | Esophagus | ESCC | response to virus | 238/8552 | 367/18723 | 6.65e-14 | 3.32e-12 | 238 |
| GO:00516075 | Esophagus | ESCC | defense response to virus | 171/8552 | 265/18723 | 3.91e-10 | 1.05e-08 | 171 |
| GO:01405465 | Esophagus | ESCC | defense response to symbiont | 171/8552 | 265/18723 | 3.91e-10 | 1.05e-08 | 171 |
| GO:00096155 | Liver | Cirrhotic | response to virus | 126/4634 | 367/18723 | 2.10e-05 | 2.77e-04 | 126 |
| GO:0051607 | Liver | Cirrhotic | defense response to virus | 84/4634 | 265/18723 | 6.02e-03 | 3.00e-02 | 84 |
| GO:0140546 | Liver | Cirrhotic | defense response to symbiont | 84/4634 | 265/18723 | 6.02e-03 | 3.00e-02 | 84 |
| GO:000961511 | Liver | HCC | response to virus | 210/7958 | 367/18723 | 7.32e-09 | 1.86e-07 | 210 |
| GO:00516071 | Liver | HCC | defense response to virus | 151/7958 | 265/18723 | 1.27e-06 | 1.85e-05 | 151 |
| GO:01405461 | Liver | HCC | defense response to symbiont | 151/7958 | 265/18723 | 1.27e-06 | 1.85e-05 | 151 |
| GO:000961515 | Oral cavity | OSCC | response to virus | 215/7305 | 367/18723 | 1.63e-14 | 9.41e-13 | 215 |
| GO:00516074 | Oral cavity | OSCC | defense response to virus | 154/7305 | 265/18723 | 1.96e-10 | 5.63e-09 | 154 |
| GO:01405464 | Oral cavity | OSCC | defense response to symbiont | 154/7305 | 265/18723 | 1.96e-10 | 5.63e-09 | 154 |
| GO:000961516 | Oral cavity | LP | response to virus | 143/4623 | 367/18723 | 7.42e-10 | 3.52e-08 | 143 |
| GO:005160711 | Oral cavity | LP | defense response to virus | 97/4623 | 265/18723 | 9.31e-06 | 1.74e-04 | 97 |
| GO:014054611 | Oral cavity | LP | defense response to symbiont | 97/4623 | 265/18723 | 9.31e-06 | 1.74e-04 | 97 |
| GO:000961522 | Skin | cSCC | response to virus | 152/4864 | 367/18723 | 5.88e-11 | 2.75e-09 | 152 |
| GO:00516076 | Skin | cSCC | defense response to virus | 107/4864 | 265/18723 | 1.84e-07 | 4.02e-06 | 107 |
| GO:01405466 | Skin | cSCC | defense response to symbiont | 107/4864 | 265/18723 | 1.84e-07 | 4.02e-06 | 107 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| ABCF3 | SNV | Missense_Mutation | novel | c.14C>T | p.Ala5Val | p.A5V | Q9NUQ8 | protein_coding | tolerated(0.4) | benign(0) | TCGA-5T-A9QA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxol | SD |
| ABCF3 | SNV | Missense_Mutation | c.541G>C | p.Glu181Gln | p.E181Q | Q9NUQ8 | protein_coding | deleterious(0.02) | benign(0.15) | TCGA-A2-A0YM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ABCF3 | SNV | Missense_Mutation | c.190N>T | p.Val64Leu | p.V64L | Q9NUQ8 | protein_coding | tolerated(1) | benign(0.003) | TCGA-A8-A075-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | epirubicin | CR | |
| ABCF3 | SNV | Missense_Mutation | novel | c.1532T>A | p.Leu511His | p.L511H | Q9NUQ8 | protein_coding | deleterious(0) | probably_damaging(0.971) | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| ABCF3 | SNV | Missense_Mutation | novel | c.23N>C | p.Leu8Pro | p.L8P | Q9NUQ8 | protein_coding | deleterious(0) | probably_damaging(0.935) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| ABCF3 | SNV | Missense_Mutation | novel | c.634A>G | p.Asn212Asp | p.N212D | Q9NUQ8 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A1F5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ABCF3 | SNV | Missense_Mutation | novel | c.634A>G | p.Asn212Asp | p.N212D | Q9NUQ8 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A1FH-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| ABCF3 | SNV | Missense_Mutation | c.543N>C | p.Glu181Asp | p.E181D | Q9NUQ8 | protein_coding | tolerated(0.4) | benign(0.022) | TCGA-E2-A1L7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD | |
| ABCF3 | insertion | Frame_Shift_Ins | novel | c.1062_1063insCCTTCCTGCCCTGATGAACACCCACCCATAATGTG | p.Thr355ProfsTer12 | p.T355Pfs*12 | Q9NUQ8 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| ABCF3 | SNV | Missense_Mutation | novel | c.1022C>T | p.Ala341Val | p.A341V | Q9NUQ8 | protein_coding | deleterious(0) | probably_damaging(0.966) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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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