|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: FGD6 |
Gene summary for FGD6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FGD6 | Gene ID | 55785 |
| Gene name | FYVE, RhoGEF and PH domain containing 6 | |
| Gene Alias | ZFYVE24 | |
| Cytomap | 12q22 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q6ZV73 |
Top |
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 |
| 55785 | FGD6 | CA_HPV_3 | Human | Cervix | CC | 3.05e-02 | 1.13e-01 | 0.0414 |
| 55785 | FGD6 | CCI_1 | Human | Cervix | CC | 1.88e-06 | 7.54e-01 | 0.528 |
| 55785 | FGD6 | CCI_2 | Human | Cervix | CC | 5.63e-09 | 1.05e+00 | 0.5249 |
| 55785 | FGD6 | CCI_3 | Human | Cervix | CC | 7.66e-20 | 1.13e+00 | 0.516 |
| 55785 | FGD6 | LZE4T | Human | Esophagus | ESCC | 6.78e-06 | 2.67e-01 | 0.0811 |
| 55785 | FGD6 | LZE20T | Human | Esophagus | ESCC | 3.16e-05 | 1.07e-01 | 0.0662 |
| 55785 | FGD6 | LZE24T | Human | Esophagus | ESCC | 7.40e-09 | 2.10e-01 | 0.0596 |
| 55785 | FGD6 | LZE21T | Human | Esophagus | ESCC | 2.92e-03 | 2.08e-01 | 0.0655 |
| 55785 | FGD6 | P1T-E | Human | Esophagus | ESCC | 6.31e-06 | 4.11e-01 | 0.0875 |
| 55785 | FGD6 | P2T-E | Human | Esophagus | ESCC | 1.23e-45 | 1.04e+00 | 0.1177 |
| 55785 | FGD6 | P4T-E | Human | Esophagus | ESCC | 2.16e-10 | 3.12e-01 | 0.1323 |
| 55785 | FGD6 | P5T-E | Human | Esophagus | ESCC | 4.29e-17 | 1.32e-01 | 0.1327 |
| 55785 | FGD6 | P8T-E | Human | Esophagus | ESCC | 1.07e-09 | 2.03e-01 | 0.0889 |
| 55785 | FGD6 | P9T-E | Human | Esophagus | ESCC | 1.23e-08 | 2.22e-01 | 0.1131 |
| 55785 | FGD6 | P10T-E | Human | Esophagus | ESCC | 1.15e-10 | 1.60e-01 | 0.116 |
| 55785 | FGD6 | P11T-E | Human | Esophagus | ESCC | 1.14e-10 | 5.39e-01 | 0.1426 |
| 55785 | FGD6 | P12T-E | Human | Esophagus | ESCC | 1.11e-14 | 2.03e-01 | 0.1122 |
| 55785 | FGD6 | P15T-E | Human | Esophagus | ESCC | 3.79e-14 | 3.22e-01 | 0.1149 |
| 55785 | FGD6 | P16T-E | Human | Esophagus | ESCC | 1.08e-13 | 1.95e-01 | 0.1153 |
| 55785 | FGD6 | P20T-E | Human | Esophagus | ESCC | 1.87e-15 | 3.85e-01 | 0.1124 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| 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 |
| ∗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. |
Top |
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:002260410 | Cervix | CC | regulation of cell morphogenesis | 84/2311 | 309/18723 | 1.00e-12 | 4.29e-10 | 84 |
| GO:00430877 | Cervix | CC | regulation of GTPase activity | 79/2311 | 348/18723 | 4.21e-08 | 2.60e-06 | 79 |
| GO:00083608 | Cervix | CC | regulation of cell shape | 38/2311 | 154/18723 | 1.86e-05 | 3.46e-04 | 38 |
| GO:002260420 | Esophagus | ESCC | regulation of cell morphogenesis | 180/8552 | 309/18723 | 5.19e-06 | 5.45e-05 | 180 |
| GO:000836018 | Esophagus | ESCC | regulation of cell shape | 92/8552 | 154/18723 | 3.00e-04 | 1.81e-03 | 92 |
| GO:004308715 | Esophagus | ESCC | regulation of GTPase activity | 183/8552 | 348/18723 | 5.34e-03 | 2.00e-02 | 183 |
| GO:002260422 | Liver | HCC | regulation of cell morphogenesis | 188/7958 | 309/18723 | 4.84e-11 | 1.82e-09 | 188 |
| GO:000836022 | Liver | HCC | regulation of cell shape | 92/7958 | 154/18723 | 1.15e-05 | 1.31e-04 | 92 |
| GO:00226048 | Lung | IAC | regulation of cell morphogenesis | 74/2061 | 309/18723 | 6.31e-11 | 1.70e-08 | 74 |
| GO:00083607 | Lung | IAC | regulation of cell shape | 37/2061 | 154/18723 | 3.35e-06 | 1.42e-04 | 37 |
| GO:00430876 | Lung | IAC | regulation of GTPase activity | 67/2061 | 348/18723 | 3.43e-06 | 1.44e-04 | 67 |
| GO:0046847 | Lung | IAC | filopodium assembly | 14/2061 | 62/18723 | 6.56e-03 | 4.60e-02 | 14 |
| GO:002260413 | Lung | AIS | regulation of cell morphogenesis | 65/1849 | 309/18723 | 2.97e-09 | 5.09e-07 | 65 |
| GO:004308711 | Lung | AIS | regulation of GTPase activity | 65/1849 | 348/18723 | 3.35e-07 | 2.83e-05 | 65 |
| GO:000836013 | Lung | AIS | regulation of cell shape | 32/1849 | 154/18723 | 3.75e-05 | 1.14e-03 | 32 |
| GO:00468471 | Lung | AIS | filopodium assembly | 14/1849 | 62/18723 | 2.46e-03 | 2.55e-02 | 14 |
| GO:002260432 | Lung | MIAC | regulation of cell morphogenesis | 38/967 | 309/18723 | 6.47e-07 | 9.76e-05 | 38 |
| GO:004308721 | Lung | MIAC | regulation of GTPase activity | 41/967 | 348/18723 | 7.39e-07 | 1.08e-04 | 41 |
| GO:000836032 | Lung | MIAC | regulation of cell shape | 20/967 | 154/18723 | 1.34e-04 | 5.35e-03 | 20 |
| GO:002260419 | Oral cavity | OSCC | regulation of cell morphogenesis | 163/7305 | 309/18723 | 5.66e-07 | 8.19e-06 | 163 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| FGD6 | SNV | Missense_Mutation | c.341C>G | p.Ser114Cys | p.S114C | Q6ZV73 | protein_coding | tolerated_low_confidence(0.13) | possibly_damaging(0.533) | TCGA-AC-A23C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | chemo | CR | |
| FGD6 | SNV | Missense_Mutation | c.2860N>A | p.Asp954Asn | p.D954N | Q6ZV73 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| FGD6 | SNV | Missense_Mutation | c.943N>G | p.Pro315Ala | p.P315A | Q6ZV73 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.996) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| FGD6 | SNV | Missense_Mutation | rs377183623 | c.3530C>T | p.Ala1177Val | p.A1177V | Q6ZV73 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| FGD6 | SNV | Missense_Mutation | c.3302N>A | p.Arg1101Gln | p.R1101Q | Q6ZV73 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-AR-A24H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| FGD6 | SNV | Missense_Mutation | rs757525900 | c.2237C>T | p.Pro746Leu | p.P746L | Q6ZV73 | protein_coding | deleterious(0.01) | probably_damaging(0.963) | TCGA-B6-A409-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |
| FGD6 | SNV | Missense_Mutation | c.4124N>G | p.Glu1375Gly | p.E1375G | Q6ZV73 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A1FU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| FGD6 | SNV | Missense_Mutation | c.1370N>T | p.Lys457Met | p.K457M | Q6ZV73 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.921) | TCGA-C8-A12K-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| FGD6 | SNV | Missense_Mutation | c.2613N>C | p.Lys871Asn | p.K871N | Q6ZV73 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-D8-A147-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD | |
| FGD6 | SNV | Missense_Mutation | c.4249N>A | p.Ala1417Thr | p.A1417T | Q6ZV73 | protein_coding | tolerated(0.07) | benign(0.146) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |