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Gene: FAM3A |
Gene summary for FAM3A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FAM3A | Gene ID | 60343 |
| Gene name | FAM3 metabolism regulating signaling molecule A | |
| Gene Alias | 2.19 | |
| Cytomap | Xq28 | |
| Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | P98173 |
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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 |
| 60343 | FAM3A | LZE2T | Human | Esophagus | ESCC | 1.19e-07 | 5.92e-01 | 0.082 |
| 60343 | FAM3A | LZE4T | Human | Esophagus | ESCC | 3.10e-12 | 2.76e-01 | 0.0811 |
| 60343 | FAM3A | LZE7T | Human | Esophagus | ESCC | 4.96e-10 | 6.52e-01 | 0.0667 |
| 60343 | FAM3A | LZE8T | Human | Esophagus | ESCC | 4.28e-09 | 2.57e-01 | 0.067 |
| 60343 | FAM3A | LZE20T | Human | Esophagus | ESCC | 9.24e-13 | 4.40e-01 | 0.0662 |
| 60343 | FAM3A | LZE22T | Human | Esophagus | ESCC | 8.71e-06 | 6.35e-01 | 0.068 |
| 60343 | FAM3A | LZE24T | Human | Esophagus | ESCC | 9.46e-38 | 1.15e+00 | 0.0596 |
| 60343 | FAM3A | LZE21T | Human | Esophagus | ESCC | 8.53e-07 | 4.68e-01 | 0.0655 |
| 60343 | FAM3A | LZE6T | Human | Esophagus | ESCC | 4.80e-04 | 1.12e-01 | 0.0845 |
| 60343 | FAM3A | P1T-E | Human | Esophagus | ESCC | 7.76e-32 | 1.24e+00 | 0.0875 |
| 60343 | FAM3A | P2T-E | Human | Esophagus | ESCC | 6.63e-45 | 7.42e-01 | 0.1177 |
| 60343 | FAM3A | P4T-E | Human | Esophagus | ESCC | 2.64e-36 | 7.47e-01 | 0.1323 |
| 60343 | FAM3A | P5T-E | Human | Esophagus | ESCC | 6.15e-20 | 2.80e-01 | 0.1327 |
| 60343 | FAM3A | P8T-E | Human | Esophagus | ESCC | 4.42e-31 | 5.38e-01 | 0.0889 |
| 60343 | FAM3A | P9T-E | Human | Esophagus | ESCC | 3.03e-26 | 6.38e-01 | 0.1131 |
| 60343 | FAM3A | P10T-E | Human | Esophagus | ESCC | 1.01e-54 | 8.02e-01 | 0.116 |
| 60343 | FAM3A | P11T-E | Human | Esophagus | ESCC | 1.67e-18 | 7.18e-01 | 0.1426 |
| 60343 | FAM3A | P12T-E | Human | Esophagus | ESCC | 2.07e-56 | 9.65e-01 | 0.1122 |
| 60343 | FAM3A | P15T-E | Human | Esophagus | ESCC | 5.59e-40 | 6.34e-01 | 0.1149 |
| 60343 | FAM3A | P16T-E | Human | Esophagus | ESCC | 2.64e-25 | 3.91e-01 | 0.1153 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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:00059969 | Esophagus | ESCC | monosaccharide metabolic process | 159/8552 | 257/18723 | 1.11e-07 | 1.81e-06 | 159 |
| GO:00193189 | Esophagus | ESCC | hexose metabolic process | 147/8552 | 237/18723 | 2.63e-07 | 3.94e-06 | 147 |
| GO:00028318 | Esophagus | ESCC | regulation of response to biotic stimulus | 191/8552 | 327/18723 | 2.12e-06 | 2.45e-05 | 191 |
| GO:000283212 | Esophagus | ESCC | negative regulation of response to biotic stimulus | 72/8552 | 108/18723 | 8.36e-06 | 8.11e-05 | 72 |
| GO:00060069 | Esophagus | ESCC | glucose metabolic process | 119/8552 | 196/18723 | 1.51e-05 | 1.36e-04 | 119 |
| GO:00442626 | Esophagus | ESCC | cellular carbohydrate metabolic process | 160/8552 | 283/18723 | 1.43e-04 | 9.66e-04 | 160 |
| GO:00160514 | Esophagus | ESCC | carbohydrate biosynthetic process | 117/8552 | 202/18723 | 2.96e-04 | 1.79e-03 | 117 |
| GO:00620129 | Esophagus | ESCC | regulation of small molecule metabolic process | 184/8552 | 334/18723 | 3.11e-04 | 1.85e-03 | 184 |
| GO:00450885 | Esophagus | ESCC | regulation of innate immune response | 125/8552 | 218/18723 | 3.34e-04 | 1.96e-03 | 125 |
| GO:00507775 | Esophagus | ESCC | negative regulation of immune response | 112/8552 | 194/18723 | 4.67e-04 | 2.62e-03 | 112 |
| GO:000268316 | Esophagus | ESCC | negative regulation of immune system process | 231/8552 | 434/18723 | 8.48e-04 | 4.36e-03 | 231 |
| GO:00463643 | Esophagus | ESCC | monosaccharide biosynthetic process | 52/8552 | 82/18723 | 9.03e-04 | 4.61e-03 | 52 |
| GO:00109065 | Esophagus | ESCC | regulation of glucose metabolic process | 71/8552 | 119/18723 | 1.46e-03 | 6.92e-03 | 71 |
| GO:00193193 | Esophagus | ESCC | hexose biosynthetic process | 49/8552 | 78/18723 | 1.69e-03 | 7.81e-03 | 49 |
| GO:00061096 | Esophagus | ESCC | regulation of carbohydrate metabolic process | 101/8552 | 178/18723 | 1.89e-03 | 8.52e-03 | 101 |
| GO:00458245 | Esophagus | ESCC | negative regulation of innate immune response | 45/8552 | 71/18723 | 1.98e-03 | 8.90e-03 | 45 |
| GO:00106755 | Esophagus | ESCC | regulation of cellular carbohydrate metabolic process | 83/8552 | 146/18723 | 4.24e-03 | 1.69e-02 | 83 |
| GO:00060943 | Esophagus | ESCC | gluconeogenesis | 46/8552 | 75/18723 | 4.54e-03 | 1.78e-02 | 46 |
| GO:00192168 | Esophagus | ESCC | regulation of lipid metabolic process | 172/8552 | 331/18723 | 1.20e-02 | 4.02e-02 | 172 |
| GO:000599612 | Liver | Cirrhotic | monosaccharide metabolic process | 104/4634 | 257/18723 | 1.74e-08 | 6.32e-07 | 104 |
| Page: 1 2 3 4 5 6 |
| 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 |
| FAM3A | SNV | Missense_Mutation | novel | c.416N>A | p.Met139Lys | p.M139K | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-GI-A2C9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | SD | ||
| FAM3A | deletion | Frame_Shift_Del | novel | c.694delG | p.Glu232ArgfsTer163 | p.E232Rfs*163 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |||
| FAM3A | SNV | Missense_Mutation | rs35985994 | c.7N>T | p.Arg3Cys | p.R3C | protein_coding | deleterious_low_confidence(0) | benign(0) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| FAM3A | SNV | Missense_Mutation | c.350G>A | p.Arg117His | p.R117H | protein_coding | deleterious(0.04) | probably_damaging(0.997) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| FAM3A | SNV | Missense_Mutation | novel | c.182N>T | p.Ser61Leu | p.S61L | protein_coding | tolerated(0.12) | benign(0.006) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| FAM3A | SNV | Missense_Mutation | novel | c.601N>A | p.Gly201Arg | p.G201R | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AX-A3FT-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| FAM3A | SNV | Missense_Mutation | novel | c.588N>A | p.Ser196Arg | p.S196R | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| FAM3A | SNV | Missense_Mutation | novel | c.467N>G | p.Glu156Gly | p.E156G | protein_coding | tolerated(0.14) | benign(0.054) | TCGA-D1-A175-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD | |
| FAM3A | SNV | Missense_Mutation | c.715N>T | p.Arg239Trp | p.R239W | protein_coding | deleterious(0) | probably_damaging(0.921) | TCGA-D1-A17Q-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| FAM3A | SNV | Missense_Mutation | rs782379297 | c.725N>T | p.Thr242Met | p.T242M | protein_coding | tolerated_low_confidence(0.06) | benign(0.014) | TCGA-DI-A2QY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | CR |
| Page: 1 2 |
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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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